If the paint is properly polished out, wax will still protect it whether it is clearcoated or not.

Why are you talking about putting wax on dull areas of the car, why would you bring that up? Maybe you should change your original statement to "if your paint isn't polished, do not wax it".
Yes, the paint would be better protected by new clearcoat, which would then be the sacrificial layer during polishing, etc., but there is no reason to give up on paint that can easily be polished and waxed...