If it has to be natural magic - then let it be natural magic. He wraps it up and gives it to her, and everyone else - a latent ability to alter one's shape in gendered ways, if and when a person is drawn to that notion. And to change it back, as many times as they want, in case there are times like with this girl when it might be easier that way.

He builds it right into the universe, but makes the magic attach to individual people as they're born (or hatched), in case they travel to other universes like he has somehow done. And he decides that next time he gets a prayer like this back home, he's doing something similar. If he's ever back home again.