I can't help but notice Noah stated that no one knows what Sylar looks like; the Season 3 flashback episode directly contradicted this, showing Noah and Elle spying on Sylar when he was first experiencing his new abilities (Elle even interacted with him more than once, so she would certainly know what Sylar looks like). This is more of a problem in that third season episode, though (IIRC, there were a few details in that episode that seemed inconsistent with what was presented in Season 1).
I'm not sure, but I think that Sylar still went under his real name (Gabriel Gray) in that episode. The Company probably didn't know that Sylar was the exact same person until later.