WMG: The Witches

Granny would become a new GHW in the future
Not immediately, but after they return to Norway and conquer the castle. Then, she would lead the two species to co-exist.

The protagonist is Mr. Bobo.
I know that in the end the unnamed protagonist (this is for the book, I've never seen the movie) is still a mouse, but this is wild. Perhaps becoming a human again made him a crazy old man. This could explain his ability to communicate with the mice. And of course, his childhood dream was to have his very own Mouse Circus. Also, if you merged the universes, the Other Mother could totally be a Real Witch.

The Grand High Witch's "frying" powers are the same as Matilda's telekinesis
The Grand High Witch was very clever from birth but, like Matilda, left her brain power unused and began to be able to spring rays from her eyes, like Matilda. The GHW, however, was never placed in an environment where she could use her mental capacities, and she kept her power, bettering with time until she could not only merely push or hold things from the distance, but even burn them.