Spoiler answer for above
Well, it's not that we didn't find Gaius' body at the end of 2.0. We never even got the opportunity to look for it as the place was crumbling around us. Actually, the last our character saw of Gaius, he was still alive. It's just that even we wouldn't have survived the Praetorium collapse unless a lot of chance things had happened. Heck, the Alliance was on the verge of thinking we didn't make it out until they actually saw us. Given that the XIVth Legion didn't act like Gaius was in control of it afterwards, it's a pretty safe assumption to make that he was dead even without a body.

That said, given that Gaius was the one who was running the place, I don't think it's too far fetched to suppose he knew of other ways to get out of there. As far as opportunities to fake your death go, it's a really good one to take advantage of. It's not like people are going to look for you if they know you're dead.

What him being alive really puts a spin on is his "Here my conquest ends" line. It comes off pretty well as a "last words" line, but it also can work as Gaius deciding that's not the route he'll be taking from now on...

As far as how much Gaius knows about the Ascians goals, it's pretty hard to beat the exchange he has with Lahabrea about it right before Ultima goes off.