You will have to lower the front end first as if you try and lower the rear end, the roof will pivot around the front actuators near the bed, and you will bend the roof (this could also be an issue if you tried all 4 at once and they get out of sync).
Having the rear end taught while you lower the front will provide some side to side stability from the liner, but nothing in the front to back direction - and once you start to drop the front end I feel like there will be a tendency for the whole roof to slide forward. Once this happens, I am not sure how you would recover.
Is there a reason you don't want the lift panels, or some approximation of the lift panels? It seems to me that this would solve most of the identified issues - shear, roof alignment and safety when the roof is up and is obviously a proven system.