It very clearly states that that character advance (Fearful Reputation Trait) requires an elite advance to qualify. It is very unambigious, in my opinion. It also sells for a whooping 1500xp to buy. I think it is safe to say that although this is offered at whatever Rank the player chooses to substitute it for (as early as Rank 1, with GM approval), it is far from being intended as an early-game character advance.
Even if you were to eschew the regular prereqs. and offer it (Fearful Reputation) up as an Elite Advance (which I see no reason for doing), going by the base rules, that'd put it at an amazing 3000xp for a single advance.
As it is right now, it is clearly intended as a senior Manhunter advance; After all, Boba didn't become so Fett when he was still a little maori youngling.
Something I think is far stranger is the fact that Peer (Underworld) and Good Reputation (Underworld) is so tied to the Manhunter; After all, we are talking about someone that is just as likely to work for Law Enforcement as for a Crime Boss (entirely dependant on character). But that's somewhat beside the point. After all, it is a game mechanic, and whether you gain the +10/20 FE bonus due to fear, respect or reverence if somewhat moot.
Addedum: I started looking at all the prereqs, preparing to make an argument as to whether Fearful Reputation is even worth it, leaning strongly towards a "no". After all, let's tally the prereqs: First you need Peer (Underworld), which is 500xp, to qualify for Good Reputation (Underworld) - which has to be taken as an Elite Advance. The cost of Good Reputation (Underworld) would be a minimum of about 1000xp; possibly more, but it's hard to determine as nobody has this as a base advance. But you also need 50 Fellowship to qualify for Good Reputation (Underworld); so let's just assume you had very good rolls and took a predominantly Fellowship-boosting Origin path, for the sake of simplicity. But we're not done. You also need not just Intimidate, but Intimidate +20 to qualify for Fearful Reputation. Depending on what Career you start as, you will have to pick some or all of these as Elite Advances. The best option here would be to pick an Arch-Militant, who starts with Intimidate and could pick up Intimidate +10 and Intimidate +20 on Ranks 2 & 3 respectively, for a total of 400xp. The second-best would be to start with a Navigator, picking up Intimidate, Intimidate +10 and Intimidate +20 at Ranks 1, 2, and 3 for a total of 500xp. This would however put off taking the Manhunter Alternate Career Rank until Rank 4 at the earliest. The third-best option appears to be Void-Master, who could pick up Intimidate at Rank 2, and Intimidate +10 and Intimidate +20 at Ranks 6 & 7 respectively, for a total of 500xp.
And THEN you would be able to get the Fearful Reputation advance as a Manhunter, after investing a grand minimum of 3400xp (and the approval of 1 Elite Advance by your GM), or as much as 4000xp or more (and the approval of an amazing 4 Elite Advances by your GM). No matter how you cut this, Fearful Reputation is intended to be taken well into your character's career. No matter what, there's no realistic chance of you having it before Rank 4ish.
But like I said, I was heavily leaning towards this simply not being worth it, at least not in terms of mechanics, when I started tallying this. But then I checked what Fear 1 actually does. Needless to say, the scum of the galaxy does generally not have any stellar Willpower modifiers. Kick down the door of a bar, I can see half of them shooting themselves in sheer desperation, turning on their friends in an effort to sell them out, or climbing up the inside of a garbage chute trying to flee from you.
Fearful Reputation is a significant investment; obviously intended as such, and rightly so. I see no issues with the cost or the mechanics behind aquiring it.
Not every GM hands out elite advances solely on request. Several insist on in game activity to justify the character acquiring said talent. But if the character has what it takes to be an elite manhunter that shouldn't be an issue.
I find that the Rogue Trader book in particular is very different to Dark Heresy in it's approach to Elite Advances. Dark Heresy appears to be very much "Elite Advances should be scarce", whereas Rogue Trader seems to sprinkle insinuations directed at the GM about giving out Elite Advances left and right all over the Rogue Trader books.
Which in my opinion is a good thing, so don't get me wrong. Elite Advances and the books encouragement to make use of the Elite Advance mechanics when appropriate is basically a carte blanche to deviate from the set rules as a GM sees fit - which he of course always can do, but a lot of GMs seem to forget this and keep to the rules.
So.. yeah. Elite Advances. They rock.
Use them liberally. Except when the players specifically ask for them.
Then they're probably up to shenanigans.