Yeah, I don't recommend this mod, specifically because of that (and because I'm sure it wouldn't work with permanent werewolf mods). I recommend my own take on this mod, which I specifically designed to take controllers and permanent werewolf mods into account
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I'd kinda want a simpler way, to just have 'revert form' ability like vampire lord has
https://www.nexusmods.com/skyrim/mods/91488