I was able to set up SpawnConfig_User.xml and add dimensionExcluse to all EnderZoo MOBs.
Considering that Aether was a popular mod and that EnderZoo MOBs in The Aether radically change the dimension, I imagine when Aether II development advances past knowledgeable testers, requests or questions on how to make this change will become more common. EnderZoo in either of these zones breaks gameplay by both having overpowered mobs and if you manage to kill them, overpowered drops.

Please set the default configuration so that EnderZoo mobs are disabled in The Aether, as they appear to be in Twilight Forest: