FEAR 2 and Doom3 were exceptions. in FEAR 2 artifacts around lights would occur when using AF through the control panel. in Doom 3 forcing AF through the control panel did nothing. of course that could have changes after all these years.AF pretty much always works through the driver control panel, from my experiences.
You are correct, especially in UE3 games, as most of them completely lack any in game AA support. I know Mass Effect 1 was notorious for this. I haven't tested it with my 570 though to see if it's still a huge hit.I believe it's usually more efficient to do it through the application's in-game settings than forcing through the driver.