If you destroy the wizard tower first, the ground opponents inside the fortification will remain there, unharmed. The opponents don't 'come out' of the tower like they were intended to actually be inside; the tower was just placed in a fortification that also had ground opponents in it, so they overlap. The ground opponents ignore the obstruction since they were not designed to work around it, but your character can not move or attack through the structure, since the game does check that.
You do get a little more experience doing the ground portions of the flying fortresses first, but not because there are more opponents. The anti-dragon structures give a fixed amount of experience, so if you delay taking them out you get more experience from ground opponents; if you level up first on the anti-dragon defences, you get slightly less than you could have from the ground opponents. For example, on level 30 and 33 you get 928 experience points for a ballista or wizard's tower in Keara's flying fortress.
In D2:ED I also cleared out the dragon defences first, as much as possible. That is part of the reason I did most of the human sections first in DKS.
