Well, he is the President. He's probably pretty high up amongst the Patriots, if not the highest-ranking human member. You'll notice how he never refers to anybody specific being above him in the group, just a shadowy "they" that enabled him to claim the Presidency in exchange for loyalty. He knows about GW's existence, but only that it's an advanced computer system, not both an AI and his boss.
That's the thing, though, He's working with Solidus in order to force the Patriots to accept him as a member. Then he does that talk about being like a chess pawn, and even if the pawn gets promoted to a queen it's still a playing piece, and he doesn't like that, and essentially gets betrayed by Solidus who tells him a playing piece can never become a player.
His analogy breaks down later because he then talks about having the power of a king, but he does strike me as a little bit unhinged...
It may just be he has different nanomachines than the military ones which are the ones said to have that lalelulilo side-effect. Ames is referred to as Colonel by Ocelot.
Ah well, just a "hey this is interesting" thought that struck me while playing.