I can't think of in any way the dungeons have been edited to work with squadrons. The reason mechanics only target the player is because squadron NPCs are coded as pets. Theoretically the groundwork is already set so long as there isn't a mechanic that needs to be done while you're disabled that isn't as simple as kill something.

That being said, I doubt they'd be able to do any dungeons in Heavensward and beyond. Damage really ramps up, especially since the NPCs don't dodge anything, and the healer AI is absolutely awful.