Just my thoughts
I didn’t want to post because I’ve no real knowledge in this, but here I go.
I would say that yes, an aerfoil can expect to have flow seperation over the rear portion of the chord when it is close to the max CL point. Even though there is no meaningful contribution of lift from this part of the upper surface, the lower surface is still providing lift along the whole chord.
The snatch that you refer to would not happen because the ailerons are linked. But there would be a force on both ailerons trying to force them up, but since they are linked, one will not go up and the other down. This force is from the positive pressure on the underside of them. I seem to recall that both aelerons will float up in flight for the reason that the resultant force on them from upper and lower aerfoil pressures is up.
The response from SNS3Guppy deals mostly with laminar flow, when he says flow seperation often about 30% chord. I’d have to say that perhaps it’s laminar flow changing to turbulent flow within the boundary layer at about 30%, and what you say I agree with. The laminar flow usually degrades to turbulent flow, which is not actual seperation. In fact the extra energy in the turbulent flow helps keep the flow attached to the upper surface. And as said, this is why boundary layer energizers are often added to wings, and in fact the slots in flaps do the same thing by injection of hi energy air. I do not think the flow over these flaps are laminar, by someone can correct me. Once this turbulent flow can no longer stay attached, the flow seperates, and you get the tufts on an upper side of a wing start to steam backwards in places, as you described.
Now you ask how an up aeleron can provide a down force in separated flow, I will really go out on a limb here, and say that it can’t. It’s the aeleron on the other side that goes down and raises it’s wing.
And now…..this is from my general knowledge….so take with a grain of pepper somewhat!!
Hawk