What did Tony know that he shouldn't have known? I don't remember him saying anything about something that he didn't have knowledge of?
I believe Tony is supposed to have known about the bioweapon all the time. As I noted above, the writers stopped production to rework the scripts for episodes 19 and 20 in an effort to have this sequence make sense. We'll see how well they did shortly.
Is Tony part of this overseer group?
Whenever I see the term "overseer", I think of the short-lived TV show Alien Nation. If you saw the show, you'd understand. If not, I can't explain it adequately.
But I don't think Tony is higher on the "food chain" of the cabal than Emerson was.