Occasionally Snarky and Meta

That's generally my assumption about Troy's characterization, and it's a good way to reconcile his behavior early on with his behavior later in the series. I don't think it's necessarily what the writers initially intended -- I doubt Harmon thought of him as a closet geek when he conceived of the character -- but in retrospect it's a good explanation, and I think it has some support from later episodes (e.g. in the S2 Halloween episode Abed is clearly the one who's more comfortable being a geek, whereas Troy's still adjusting).