There are some hints that he might have. Late in the game Urwald says that he thinks there is some trickery in Thomas's soul. Also if you break into Terk's office and read Thomas's file after learning his secret, Shawn will say that he knows what Thomas lied about but wonders who found out... he says it certainly wasn't Terk which I agree with. I would think the most likely answer is Urwald. Urwald is presumably a master of recognizing disguises because he uses them himself. That is to say Urwald may have wanted Thomas in his class not because he didn't think Thomas would make a good paladin, but because he thought Thomas's strength was being a rogue. Does that seem right?

I kind of got the same impression - that Urwald at least suspected something to that effect.

He couldn't be a paladin for that reason - the ghost tells him as much. Rogue, on the other hand, is a natural fit to it.

If Thomas was going to admit the deception to anyone, it would be Moira, but Urwald is by far the most likely to recognize it on his own. The only other likely option is the Librarian, who is shown to be more than just a book-arranger throughout the game, also knows how to keep their mouth shut, and who Thomas spends the most time around outside of class and might inadvertently give something away to since he won't be as guarded at those times.

Due to both the librarian and Thomas not being the most sociable types, I doubt they would have talked much. He probably talks with Sean more than anyone, and at the start he definitely doesn't appear to really want to talk.

What I still don't quite understand is exactly why Thomas used that particular disguise. I can understand being disguised due to wanting to secretly join the school etc. (so others don't find out about the whole Rogue thing, since the Paladin thing was out). On the other hand, it WAS a damn good disguise, so maybe that's the only reason? Thomas IS very meticulous, so possibly calculated that this way it would be nearly impossible to identify the real person under the mask...?

I haven't played in a while, but I don't recall ever getting into the nitty gritty of the details at any point - it was more like "ccouldn't be a Paly, disguised myself and became a Rogue". At least from what I remember (?).

The librarian is definitely observant. Also very wry and cynical. Possibly one of my favourite characters in the game.

Going even more OT: Wasn't he also part of that group of heroes that saved the place, along with The Creepy Guy and gang? Though he may have stayed behind to guard the fort, so wasn't in the final battle or something to that effect IIRC. So, I'd say he was most likely the Rogue of that team.

It makes sense that the librarian would have known about it, for the reasons Garran suggested. On the other hand, just noticing it wouldn't be enough. The librarian would also have had to tell someone, which is the part that seems less likely. I doubt the librarian would have cared at all, and someone as anti-social as the librarian would have to care a lot about something to tell anyone.

I'd say the only reason was indeed that it was a great disguise. All he cared about was whether or not the disguise would work. And it did indeed fool everybody except maybe Urwald and maybe the librarian.

Urwald wouldn't have told Terk, I'm sure. And Terk wouldn't have believed him if he had.

Maybe the librarian would have; I don't think anyone knows anything about how he and Terk feel about each other.

I'd say that whoever assigned the students to their dorm rooms would have had to know. It's a bit much of a coincidence that Thomas was the only student with a room to himself. (Well, Aeolus initially was too, but then Shawn became his roommate.)

And, of course, Terk knew about the sleeping arrangements too; he was the one who informed Shawn that he'd be rooming with Aeolus.

The headmaster?

That's a character who's mentioned many times but we never see, except for a painting of him in Urwald's classroom and a statue of him in the hall of heroes but we never see him in person. I guess it's possible he was the one who knew.