Make no mistake, I think Lance is barely a threat for top 10 when all is said and done and will get beat handily in the mountains (not sprinter throttled, but due to the Team Time Trial, some mountain specialists will be looking to up the pace in all mountain stages and I think Lance will get dropped before a lot of other serious contenders). Contador is defniately the top Astana GC guy, no question about it. It's silly to think otherwise (although I'll admit I have no idea how Kloden will fit in to all of this)
I just think that Lance at the very least THINKS he's the team leader and that it will cause Contador to move to a team, eventually, where he is not sharing domestiques with anyone. He will win a lot of grand tours at whatever team gets him and JB will regret not bowing to his every whim.
Of course I could be wrong and Contador could be quite content. I doubt it, however. Incidentally Stage 3 at the tour de france didn't affect my opinion one way or the other.