I predict that Brainwarp is simply alternating the timing of the two displays, and otherwise they work as normal. Practically this means a fast moving object in the field of stereo overlap will have ghosts as each eye will perceive it in a slightly different place. I’m guessing the brain can compensate for this and treat the older image as an artifact many of us are already used to seeing with fast moving objects on conventional displays.
EDIT: As the newer image hits the panel, the alternate panel will already be winding down and the screen going dark in preparation for the next refresh, so the disruption should be minimal. In theory.