My hypothesis does NOT insinuate any of the things you say it insinuates. What I am saying is if the two GPUs are not synched to render at equal time differences, then you will end up with the two rendering at odd time differences. They will render at approximately the same speed, but if they are not synchronized at exactly even time differences, you will end up with some sort of microstutter. As an illustration, I will write an example of two possible GPUs rendering a scene at exactly the same rate:
GPU1: 0ms, 60ms, 120ms, 180ms, 240ms.
GPU2: 10ms, 70ms, 130ms, 190ms, 250ms.
Add them together, and you end up getting frams at this interval:
0ms, 10ms, 60ms, 70ms, 120ms, 130ms, 180ms, 190ms, 240ms, 250ms.
1.2.....1.2.....1.2.....1.2.....1.2
(with each dot symbolizing 10ms of time passing)
Even though you are rendering on an average of one frame every 30ms (each processor taking 60ms to render its half of the frames), due to the two processors not being synchronized you end up having every other frame taking 10ms to render, and the other frames taking 50ms to render. This is the cause of microstutter, which is the bane of AFR (albiet this is an extreme example of it)
It would be difficult to correct this so that the synchronization works correctly. You don't know ahead of time how long the first GPU will take to render the frame, so you won't know when it will be half done to start rendering the second frame on the second GPU. If you could design a method to determine when the first GPU is half done rendering the frame it is currently rendering, you coudl then have a signal sent to the second GPU to begin rendering its frame (which would in turn send a signal back to the first GPU when it is half done rendering its frame). I would probably set it less than 50% complete to account for signal delay, but this is the only way I can think of correcting the microstutter off the top of my head.