It depends.
Some things can be deactivated, some can not. The things the game picks up on every load could be deactivated I think, like crafting recipes. Other things too, like extensions to existing character scripts. But things like story code cannot be disabled.
And I have some additional skills in the mod and don't know what happens if the game expects them but does not find them anymore.
Your helmet bug is a really weird one. I do not have understanding of graphics or 3D stuff, I only learned that there are 'bones' used as anchors to attach some graphical stuff to some other stuff. Like the effect I play when the Control skill is used. I think that gear might be attached to those bones too. So maybe this 'head bone' got shifted up by something.
The played effect is a possible source of that bone shifting in my simple understanding.
