.. vary in a slightly different way, will they recognize each other as such?
Being strict in recognizing the other is a feature, not a bug. You want to obtain a stable Nash equilibrium.
If you don't recognize your opponent as a copy of yourself because he's written in C++ and not Java, or because he uses iteration and not recursion, then you're acting sub-optimally (unless those things matter of course!).
Suppose that Red got to move first. There are some games where moving first is terrible - take Rock Paper Scissors for example. But in this game, moving first is great, because you get to narrow down your opponent's options! If Red goes first, Red picks 'A', and then Blue has to pick 'B' to get a cookie.
This is basically kidnapping. Red has taken all three cookies hostage, and nobody gets any cookies unless Blue agrees to Red's demands for two cookies. Whoever gets to move first plays the kidnapper, and the other player has to decide whether to accede to their ransom demand in exchange for a cookie.
What if neither player gets to move before the other, but instead they have their moves revealed at the same time?
Pre-Move Chat:
Red: "I'm going to pick A, you'd better pick B."
Blue: "I don't care what you pick, I'm picking A. You can pick A too if you really want to get 0 cookies."
Red: "Okay I'm really seriously going to pick A. Please pick B."
Blue: "Nah, don't think so. I'll just pick A. You should just pick B."
And so on. They are now playing a game of Chicken. Whoever swerves first is worse off, but if neither of them give in, they crash into each other and die and get no cookies.
So, The Question: is it better to play A, or to play B?