I think it probably came down to the fact that with full flap,plus wind over deck then the front aircraft needed to get airborne in a `reasonable` attitude` so they didn`t clout the tail/fins on the deck as they left the ship.Most aircraft have a much lower `attitude` with full flap,and also usually a lower stalling speed.Once clear of the deck then one would gradually raise the flaps. I`m sure J D had given it a bit of thought and tested it out beforehand..