No, AFR cannot be fixed. If you don't notice it, you either have always more than 50-60fps, a CPU bottleneck or your perception is just different.
AFR will always microstutter below a certain fps threshold that varies from game to game. Usually it's about 50.
When I am using the same game, with the same settings, on the same monitor, with the same 60fps vsynced and one system stutters while the other does not, it can't be my perception that changes, can it now?
Also as I specifically mentioned, if I enable MSI AB's framerate limiter and keep vsync enabled, this stutter goes away. Again on the same system, same settings.
Yes AFR will stutter worse than a single gpu solution if the framerate is low, but that's why you're getting two gpus in the first place, so the framerate does not drop.
Even my old 5850 CFX solution, can still provide some good gaming settings without stutter. With one card this would be impossible.