In the end the developers of the game would determine the extent to which players could use mods to control their characters or automate processes. If they don't want you to be able to do something, it's as simple as not coding/giving you the API functions to do it.

There is, in fact, a broad spectrum of mods that don't play for you:
customized frames/aesthetics
customized button maps
damage meters
enmity meters
bag/inventory mods
recipe book mods
encyclopedia mods, such as for gathering
chat mods

WoW itself has some classic cases of mods whose API backbones were disabled because it was determined they trivialized certain game mechanics (one mod used to draw safe zones as transparent circles on the floor). If the developers undertake UI customization I'm sure they'd understand that they have a responsibility to maintain game integrity.