I dont know about ATI (but im guessing its similiar), With Nvdia drivers you can set a Profile that relates to a particular .exe (lfs.exe). So every time you start that .exe your gfx settings are changed automatically for that game, when you exit the game your default settings are reverted.
The only reason i would like AA + AF supported in game is that some times when i Shift-F4, to check a website or somthing, and then go back to the game my AA + AF turn off and i have to restart the game.