Um, Yes you can. I just tinkered with it and I was able to reskin Tholian units. I didn't test every type of mob, but all the ones I tested worked fine. I was able to reskin a battleship group as a Borg Diamond, and am ensign group as Boslics.hehe, he don't know me very well do he?
Its the other way round. you cant reskin a non tholian ship to look tholian or reskin one type of tholian ship to look like another.