There are sometimes missing or extra chips on the bottom half of the board, as well as various jumpers installed on various places on the board.
I haven't had a chance to really go through and document the differences, but there is some atari paperwork on it--it might be in the troubleshooting guide; I can't quite recall if that's where I saw it or if it was somewhere else.
Atari did make a "universial" board, which appears to be fully populated.