Mine drain a couple of inches above the waterline. The floor of the cockpit is not that far above the waterline, maybe 15" given the relatively low freeboard of the
boat. I never get water back flowing into the cockpit. At most I hear a gurgle now and then when they are buried on the lee side.
I agree that most scupper are inadequate to quickly draining the cockpit, but that's really only an issue if you have a very large cockpit. The floor area of mine is about 3'x6', pretty small. If the cockpit got swamped everything above the floor cutout would drain out the back. Bottom line is that if your cockpit swamped and it was an issue for
boat handling/safety then you need to find a way to drain it quick if it's not engineered to.
I have some friends who circumnavigated on a narrow-butt double ender that did not have adequate buoyancy in the stern and they would occasionally get pooped in big seas. Their solution was to inflate the
dinghy in the cockpit well on long passages which kept it from filling with water. Said it worked well despite the inconvenience.