I'd imagine that most (if not all the) magic taught to the Vashoth or the Dalish protagonist wouldn't likely be part of the Circle curriculum, and would be seen as making the mage a maleficar, as even shapeshifter Morrigan was viewed as such by Alistair and Wynne.
I don't know, Merrill seemed to have learned mostly spirit and primal magic as the first of the clan, and most specialized stuff the Dalish learn seem to be nature-related, which is probably not something the Chantry bans. They don't really seem to ban that much outside of blood magic and things closely related to blood magic, in all honesty.
As for the Vashoth, we don't know where they were trained. Since the Qunari don't train their mages I can't see them being taught by them- most likely it was by other Vashoth mages of Human mages, neither of which are likely to teach in-depth forbidden stuff, because they probably wouldn't know any themselves.
I always assumed that Morrigan was a Maleficar due to knowledge and practice of things like the dark ritual, which came very close to blood magic, not necessarily her shapeshifting.