If you have already cleared an area, any running back and forth that you have to do (for merchants, or checking with NPCs about quests, etc) is a PITA if you have to keep re-killing the same opponents. Also, fighting the same opponents over and over gets boring (as does leveling for the sake of leveling, or for some superficial achievement).
From the Divinity 2 site's FAQ;
What are Flying Fortresses?
Flying Fortresses are the massive siege tools used by the Black Ring armies commanded by Damian. They consist of floating islands on which ballistae and lightning towers have been built, and where nest towers bring forth endless hordes of undead drakes and vicious Demons. Hovering monstrosities, it takes but one of these Fortresses to annihilate and entire city.
I would assume these 'nest towers' respawn opponents until they are destroyed, so there is some respawning in the game.
