I've had this thought before too.
The (entirely personal) answer I have come up with is that the Phoenix as a whole were happy to ignore the Unicorn when they were "barbarians returned" even if a minority of shugenja were concerned about this "thing" called Meishodo. Who knows what backward (inferior) beliefs they picked up in the gaijin world. But it wasn't relevant to the core of Phoenix interests.  NOW in the present, imbalances in the spirit world are rampant! What could be causing them? All Phoenix in the know put a priority on addressing this! The formerly minority of Shugenja suddenly get traction! "Its like we've been saying for generations - the foreign Meishodo magic is warping the spiritual fabric of the land!" So now it's a big deal.

It depends! 😀
Travel papers are a technicality they could nail you on. But if you are status 60 I would think you could get someone (an Emerald Magistrate?) to issue papers to you under your real identity and your false identity. How discrete are/were you? 
Being a spy for a clan is not the same as being a shinobi. Its not honorable, but no one is going to have an existential crisis thinking about the celestial order and of how Rokugan is supposed to work because a Scorpion got caught sneaking around. It might be different if you got caught "in black pajamas" sneaking into somewhere you weren't supposed to (and...OMG someone died by poison!).
Your honor definitely takes some kind of a hit by spying in the first place and your glory takes a hit for being caught.
Is it illegal? Not exactly ... I'm sure some buerrecrats try to nail you on something! But that's because a lot of people have become ticked off at you. And now want a pound of your flesh. That's not necessarily because of what it says on a moldy imperial scroll.
I personally would claim to have been seeking a romantic liaison with someone, and then swear you'd rather fight a hundred duels than share her name. At least that sounds like something a little north of disgraceful.
Good luck! I hope it worked out!

Yoshi bows deeply. “Thank you for welcoming us to your wonderful festival. Some of us were hoping to compete tomorrow. I know I am hoping to compete with the sword Yasuki-Sama.” Yoshi bows again.

There is also the Imperial Cartographers/Census Takers and Tax Collectors.

Its like any RPG. You have to work with your players so that the story/party make sense. You are not going to have a sith lord and a jedi pc in the same team...
Same in this game. You can definitely have alliances between clans for multiple reasons though. A lot of people mentioned many reasons already.
Also, I'd work with my players to make sure we are all on the same page, and then assign them Giri that have importance in the main story. Do not do as the corebook mentions and let all your players take the Giri they want, it just doesn't work. You can "discuss" with them so that everybody agrees on the Giri, but as a GM, you need to give them inputs and options for what type of Giri would make sense with the campaign you are planning.

Hostages and relatives, too.
Yes, Isawa Kaede is technically Akodo Kaede since she married the lion clan champion, but if she needed a party of samurai to go poke something, it'd be quite feasible to find the odd relative from her old family in the group too.
It's far from unheard of to have a samurai from another clan who lives in another clan's city - as a representative, ambassador, relative of a clan member (current or deceased) or an artisan of some kind who set up shop there for whatever reason (a Kakita smith who petitioned the local not-crane-but-not-hostile-to-the-crane-either lord to establish a forge there because of the quality of the local iron ore, for the sake of argument).
 
Obviously the bigger the 'problem', the more clans naturally get drawn into it. Bandits on the border of both clans are arguably dealt with by a force from both clans so there's no room for misunderstanding, gloating and hard feelings afterwards. A threat to the entire empire like a maho-sensei.....well, that's the entire Empire's problem to solve.

You could also form a party of samurai on their musha shugyō (warrior's pilgrimage), which technically makes them rōnin but lets them travel and visit all of Rokugan as a way of learning and growing. I'd say that having them still have clan schools is fair play for such a group.
Or go all-in on "special snowflakes" (as opposed to a bit, which is true of all PCs) and have the Emperor force some/all clans to send a joint group for some reason.
Another way to do it would be extending the timeframe. The party meets at, say, a Winter Court, part of their clan's respective delegations. Then they meet again, months later, because their paths lead them all to the same town. Etc.

There are three main types of adventuring parties in Rokugan.
Emerald Magistrates and their assistants. They are Imperial troubleshooters.
Clan Samurai with a few allies/friends/observers/guests from other Clans doing Samurai stuff.
Ronin who don't belong to a Clan just trying to survive.
Emerald Empire is the sourcebook with lore and adventure seeds.

Yoshi bows deeply at the departing samurai.
"Well, there is still the matter of the Crab merchant. I think we all owe Hiruma-sama a visit. I had the thought that I might turn up around diner time...are you interested in going there as a group to investigate his new find? We could meet up the sun gets low on the horizon." Yoshi looks up at the cloudy sky "Though maybe that might be difficult..."
"I do need to sign up for the tournament tomorrow. Since it is going to be open to what contestants agree to I was wondering, if you truly are not competing, if you might agree to represent me in negotiations?..." Yoshi trails off hopefully.

It depends! 😀
Travel papers are a technicality they could nail you on. But if you are status 60 I would think you could get someone (an Emerald Magistrate?) to issue papers to you under your real identity and your false identity. How discrete are/were you? 
Being a spy for a clan is not the same as being a shinobi. Its not honorable, but no one is going to have an existential crisis thinking about the celestial order and of how Rokugan is supposed to work because a Scorpion got caught sneaking around. It might be different if you got caught "in black pajamas" sneaking into somewhere you weren't supposed to (and...OMG someone died by poison!).
Your honor definitely takes some kind of a hit by spying in the first place and your glory takes a hit for being caught.
Is it illegal? Not exactly ... I'm sure some buerrecrats try to nail you on something! But that's because a lot of people have become ticked off at you. And now want a pound of your flesh. That's not necessarily because of what it says on a moldy imperial scroll.
I personally would claim to have been seeking a romantic liaison with someone, and then swear you'd rather fight a hundred duels than share her name. At least that sounds like something a little north of disgraceful.
Good luck! I hope it worked out!

::I'll toss the other option into social subtlety. Yoshi is being mindful around a surprisingly stressed out VIP::
Yoshi falls back  on basic courtesy. "Ide-sama you have not indicated if you would accept the antler from Ito-sama. Again we offer it to you..." and then a third time, "I hope you will consider accepting it. I believe Ito-sama would view it as a great courtesy..."
If Hekasu isn't interested in checking out Bakin's response. Yoshi will make an attempt... Meanwhile ... Sorachi?
::Earth3/Survival 0. I roll a success, a success with strife and a blank. failure. I confess I don't remember who this person is. ::
 

Probably. Probably not imperial law per se, but the important flaw in your 'it's-dishonourable-but-not-illegal' argument is that your presence in and travel to Toshi Ranbo was authorised by someone.
If your travel papers refer to you by your false identity, then you are travelling with no papers and no permission from the local lords, which would definitely be accepted by most factions as illegal.
 

Hekasu notices Ide Arban's eyes widen somewhat as she sees the scrimshawed antler.
"This...was made by a cousin of mine in Khanbulak," she says, "and was given to Sora-san when he walked his warrior pilgrimage, many years ago. I would not have imagined him giving it up if I had not seen it with my own eyes. I take it there is some letter to explain?"
Yoshi respectfully hands over Ito Sora's letter to the Unicorn samurai. She reads it and bows her head sadly.
"Rather more than a 'scuffle', then, I suspect. Sora-san downplays his skills with a blade but I do not imagine any common ruffian besting him easily, despite his age. I hope the village has not suffered too greatly; I have seen the wreckage 'bandits' can leave of an un-walled village too often recently on our Clan's border with the Lion. I..." she pauses. "I should not commit myself to results with so little information, but at the least I can promise to view these horses and blades and see what can be done."
"I take it these are the horses in question?" She asks, gesturing past Yoshi's shoulder to where Aruzhan and Kenshin are holding the reins of the four horses.

Arban sighs wistfully. "Then I thank you for the service you have done him and Koharu-san - and it is fitting we try and turn this last victory into a lasting legacy for the village."
She turns to her yojimbo "Aisha-san - you and Bakin-san have a far better eye for steel than I. Have a look at these blades and tell me what you make of them. Meanwhile....."
The unicorn makes her way to where Kenshin is holding Wildfire's bridle, bows, and holds out her hand for the bridle. "If I may, Kenshin-san?"
Taking the bridle, she begins a very thorough check of the horse. She begns tutting audibly and clicking her tongue like some heimin merchant whenever she sees something she is not satisfied with, but then stops abruptly as if this is was a reflex she has trained into herself. Surprisingly, she takes a knee to examine the horse's hooves and forelegs in person, squelching audibly and looking remarkably unconcerned as a mudstain spreads richly dyed fabric of her kimono.
"Not exactly Shinjo cavalry steeds, but healthy, and well-cared for, if a bit over-enthusiastically groomed." Arban says, inclining her head respectfully towards Aruzhan. "I wouldn't want to try fighting a battle on one, and the average Hida bushi would probably dislocate their backs if they tried to ride one in plate. They'd fetch a tolerable price as remounts for couriers for one of the minor clans or vassal families around here, though, I imagine. Including Sorachi-san's work should help sell them, though - you are, I assume?" She asks, looking questioningly at Yoshi.

"I do not believe I had the opportunity to meet Sorachi-san. But if you mean the tack and saddles Ide-sama, then yes. They are also from Flint Quay village and should be sold for the benefit of the village. Ito-sama was hoping to buy or trade for ashigaru armor to better outfit the village defenders in case of additional future attacks."
Yoshi bows to the Unicorn samurai.
::Air3/Courtesy1. 2 successes, an explosion with strife, and an option. I keep the a success, the explosion and the option. The explosion comes up with another option. Courtesy is my WR skill at Tier 1 so I ignore a point of strife. That results in 2 success and 2 options. I'll use the two air options to "take the pulse" of Ide-sama & Bakin by learning their demeanor and strife::

::done! Happy to help if Hekasu has strife to dump. Hekasu can remove 2 strife... :: 

I haven't mentioned anything about the jaw-cracker ... yet. Since Ito-samas health is directly tied to his fight with Kazama I am (currently) planning to share that knowledge with Ide-sama first. I kinda like these guys but I don't know that Ito-sama would want that information shared with the ronin guard first...

I'd be happy to let them do either, depending upon when in their life they were adopted.  As you say, an ashigaru promoted to the samurai class due to bravery is a completely different thing than a child adopted in recognition of generations of service.

There is a bit in Across the Burning Sands (the Unicorn Novella) when Shono has a sudden realisation that these Gaijin have their own kind of honour, even if it isn't to exactly the same code as bushido.  I'm pretty sure that they will use that as something of a precedent for all of the foreigners.

Yoshi blinks. The tries again.
"Well. As one of the Great samurai she is probably in the Grand Pavillion. We could just go over there and hope she's there. And that she remembers Ito no Asahina-sama as fondly as Ito-sama remembers her. And hope she is interested enough in dealing with our modest four-horses-and-a-sword to to welcome our interruption in whatever Ide-sama is currently doing. Or instead of just barging in we could be Courteous and take a softer approach. Set up a meeting at a time convenient to the samurai we are essentially seeking help from on behalf of Ito-sama. Make sure she's where we know her to be so we don't look like presumptive fools if in fact she is not there..."

This should be easy enough, Yoshi thinks.
...
"Most honorable merchant. These knives are delightful. I think i saw some just like these once offered by the Ide Arban-sama. You aren't related to that great samurai are you?"
...
"Spices! What is it with the prices of spices?!? They're too high, you can't find them, and then all the farmers are seasoning their food with them! How I wish Ide Arban-sama was around. I bet she could explain this to a poor confused ronin."
...
"Oh the parasol is very beautiful indeed. And I just happen to know a beautiful Yasuki lass ... who it would treasure it if a a tall ronin were to make a gift of it to her. But I have business with Ide Arban-sama to complete first. A ronin needs to be mindful of his coin purse at market. I strongly suspect though that favorable terms are at hand. Do you know where she might be? The sooner I finish that piece of business, the sooner I could return..."
::Air3/Courtesy1. I roll a blank. 2 options. &  a success with strife. Courtesy is my Worldly Ronin skill at level one. I keep the success, the options and ignore the strife. Both options go into the Yoshi-as-ninja-fund to be very subtle. Someone might remember a big ronin asked about goods, but its going to be very hard for anyone to discover I was asking about Ide Arban sama::
::Also if possible I keep and ear out for the gossip of the market.::
 

My 11-year-old son wanted to go this year as a kitsune shugenja.  I think we did alright.  As a test run, I got to make a Scorpion Clan tshirt, so we all win!


He's holding an origami shuriken, with kanji for "banishment" written on it, to throw at the various undead and oni we encountered on this spooky night.

Yoshi is happy to leave his horse in the care of Aruzhan.
"Well I already knew she would be here. No reason to panic." Yoshi mutters softly. But also no reason to meet her just yet either. Better after the competitions and I maybe look better after defeating an opponent or two. Or humiliate myself as a fool. He thinks.
Yoshi turns back toward the marketplace and starts looking for one of the merchants with the Ide mon. Perhaps I can get the information I desire another way.
 

The market is bustling, and if it were permanent would easily match the markets in most larger cities. Vendors are everywhere, hawking dried fruit, cooked bird-meat, spices, incense, cloth, carved wood, even - with a noticeable gap around the stall - a temporary forge set up by an enterprising travelling tinker repairing tools.
The more prosperous inhabitants of Uimi Mura form some of the vendors and no small portion of the customers, but the majority of the stalls appear to be villagers from the rest of Yasuki Onodera's territories, or merchants acting on their behalf. Many stalls are centred around a cart, with a 'roof' of waxed cloth to keep the rain off the goods on display - indeed most smaller stalls barely consist of anything else.
 Scattered here and there are occasional stalls clearly managed on behalf of other samurai, discreet family mons declaring their allegiance and their superior status over the heimin merchants crowded between them. The bulk are Yasuki, unsurprisingly, but there are some Daidoji, and even a few Soshi and Ide mons to be seen. The samurai making their way through the market tend (unsurprisingly) to stop at them in preference to the hiemin stalls, and most offer goods suitable for the nobility; silk for kimono, expensive sake, and carved artworks. A large 'stall' bearing scorpion heraldry on the right just before the pavilions appears to have been turned into part inn, part teahouse, and several samurai - many of whom lack family mons and have a general air of ronin - are sat under the awning watching the crowd and examining and maintaining a rather eclectic selection of bows.