The issue is, the way I read it, the frames are mis-timed because the GPU cannot fully render the frame to be displayed before the previous frame has been rendered by the other GPU. So unless you can render the frame faster somehow, the only thing you can do is remove the runt frame (which will most likely cause artifacts similar to the ones already present) or slow down the frame being delivered by the other GPU - Either way you're loosing a partially rendered frame that fraps counts as a whole frame, thus dropping the recorded average fps.
I can assure you, the GPU is not fully rendering all the frames, if it was there wouldn't be an issue with runt frames.
The way I see it, due to AFR and AMD's lack of frame metering the fully rendered frames are just not delivered evenly - aka microstutter. Runt frames are still fully rendered on the GPU, but delivered with very poor timings.
I would be very surprised if AMD was only rendering partial frames on purpose for performance advantages, and then timing the next frame to cover it up.. sounds like its more difficult to do than implementing frame metering in the first place.