(SPOILER)They were interrogating him about trying to use Vegnagun. He yels out in anger, asking "why am I being held here", and claiming "it was the only way to save the summoner (singular, so it refers to Lenne). I base this on the Eternal Calm video-sphere (where it is clearly Tidus, not Shuyin, as in FFX-2). This means he survived after he got shot, if not corporeally, then at least in spirit.
And technically, "near the end" is still during the war, until its actual conclusion. Of course I make the assumption only because it is in the game, which is considered the ultimate canon. Otherwise, I would say there are a few inconsistencies, and that Vegnagun could not possibly have been originally developed to fight Sin, but planned to only after Sin's initial appearance.