You can't set AA in launcher... it has it's setting in Launcher, but for now as far as I know, the builds don't support anti-aliasing so the option doesn't really do anything... yet. It's for the future, when the engine will have in-built anti-aliasing option. I could be wrong (better wait for confirmation from some SCP coder) but that's what I think is the situation now.
So, full screen anti-aliasing via driver force-AA options is the way to go for now.
Also, 16xAA is kinda hidden feature in (especially windows) GPU drivers - you can enable it from, say, RivaTuner, though (in OpenGL options). And NVidia's Linux driver has it as an option as well. But the difference in visual quality from 4xAA up is not often noticeable - perhaps it's noticeable in screenshots, but in gameplay it doesn't make real difference to the visuals if you se 4xAA, 8SxAA or 16xAA.