If the fairies themselves have personalities, can think for themselves, and can transform into a humanoid form, then they are too sentient to be brought in as mere companions. With the way this game is set up, there's a chance they could be brought into their own flight or qualify as a different "class" than their partner would be.

It would be possible for a magical girl to come in with her item that would allow her to transform if you wished to keep canon abilities. This item would just be like an ordinary item/weapon that allows them to transform, but if that might upset them too much (seeing their partner forced into an object), they could work together with a dragon mage of their respective flight to create a new item possibly.