There is no solid, scientific explanation for how Protectors shift into and out of dog form, just as there is no rational reason for Guardsmen to have heightened senses in their human forms, a trait that even Handlers evidence to a slight degree. The intricacies of the bonding process are not understood either, given that it can occur across a wide variety of connections (romantic, sexual, sibling, friends).
Everyone agrees that it is "some form of magic" but there is a lot of disagreement about what "magic" IS, whether it is simply a natural phenomenon we don't understand, or if it is truly some paranormal force.