First, I don't believe for a second that your time is any more or less valuable than Elias's time. To spout otherwise screams of arrogance, especially when you flatly tell him to "You should think about a solution rather than expect just me to,...", to something he, nor anyone other than you apparently, seems to BE a problem. If you don't like what's being done, go back to the original book or Houserule the Houserule.
Second, let's take a look at the most extreme possible build for a Sil 4 transport, assuming as many Triumphs and Advantage to max out HP's and Attachments. The Sil 4 Transport starts with Hull of 25, Enc 20 and 17 HP. Assuming you add a HP in both the areas that allow it, it would be 19 (yes, I know I'm doing things out of order, but the math still adds up). So, taking the Single Ion Coil engines at 2 HP, leaves 17 HP gives it no Defense a Speed of 1 and 8 SS. Speed COULD be modded up to 4 and SS up to 20, but not very likely for both, but hey, it's an Intellect 7, skill 6 (with Cybernetic Upgrades) Hotshot/Gamble/Droid-tech/Cybertech with all 5 ranks of Second Chances, Supreme Double or Nothing, all 3 ranks of Eye for Detail and Unmatched Fortune, so the dice are his b***h, so all the mods. Now with Transport Hull (got more niftys) you get Armor 1 and Handling -2 maxed out again gets Armor 3, Defense 1 F/1 R, Handling -1 and needing only 1 Pilot. No HP loss there so still at 17. Now the Hull can give Integrated Systems (twice because it's a Transport) so we'll go with a Hyperdrive and Navcomputer. Now Assembly can net 2 more Integrated Systems, we'll go with a weapon emplacement and 1 extra cargo hold. Getting escape pods, a Life Support System and Basic Sensors for a total of 1 more HP leaves a whopping 16 HP left. That's 16 MORE cargo bays plus the 1 from earlier and the 20 it starts with that's a total of 4355 Encumbrance! It's obviously worse than you thought.
Now final stats look like Sil 4, Hull 25, SS 20, Speed 4, Armor 3, Defense 1 F/1 R, Handling -1, 0 HP, 1 weapon system and Enc 4355. Now, the big thing is, what does that Enc mean? Let's assume the are hauling steamer trunks. Standard steamer trunk is about 3.35 Cu Ft and I'd hazard about enc 5. That's 871 steamer trunks at 3.35 CuFt each netting approximately 2917.85 Cu Ft of space needed. Assuming a 7 ft. ceiling that leaves about 20 ft by 21 ft needed for top to ceiling stacking. Since that's not really possible, I'll double the needed space to 40 ft x 40 ft. Not an extravagant amount of space really for a Sil 4 ship.
Big problem here...it's unique, not very good for smugglers and with a capacity that big, it would be the envy of many a possible pirate. Another is no options to upgrade anything...ever. And lastly, the GM let them build it that way. Just because the rules do not expressly forbid it, common sense should step in at some point (like not allowing a Fighter to have the 45 possible SS , 57 Enc and Passengers of 49 in the core book)
Third, many players may not be making spacestations and the like in their campaigns, but GM's might. FFG thought it important enough to add them in to the rules, so they should be gives as much weight as to the all important Sil 4 transport.
Fourth, speaking of the Sil 4 transport. This ship seems to be of the utmost importance in your games, not necessarily everyone elses'. Our group has four Sil 3's and a Sil 5. It's been established lore for a while now (though I can't recall if it's been re-stated in canon, my time is too valuable to look right now 😋) that the Light transports were not the primary sources of hauling across the galaxy, usually small companies with small amounts of freight, smugglers and the like. They were a dime a dozen and no one looked twice at them...unless they stick out like a bloated pack mule in a room full of shetlands.
My appologies if my tone is sarcastic, but it comes across that you seem h**l bent on telling Elias that what he's doing doesn't fit your game and it's his job to fix it for you, not yours. That bothers me, especially when Elias is doing 98% of all of this by himself with salamar_dree doing the bulk of the big build testing. Heck, the only thing I've contributed was "hey, appreciate the work you're doing".