FSAA is automatically disabled on newer cards if you use MRTs (multiple render targets),
I'm not saying you're wrong about this - you evidently know far more about graphics programming than I do - however, when I'm playing HL2, if I keep an eye on the per-frame texture budget (I was trying to track down the causes of the stuttering at the time), the amount of RAM given to render targets varies. This leads me to believe that MRTs are used, presumably for screens, the water effect, and a few other bits.
FSAA works perfectly well in HL2, so what part of the puzzle am I missing? I'm looking to learn here, this is an interesting discussion!