My understanding is that his evil ending doesn't do anything with Mizora. I would think and evil and powerful version of Wyll would be onboard for some vengeance, and that could get pretty dark. Killing her would be personal, so it wouldn't feel as generic. The lack of closure with Mizora frustrates me. I hate her. At least Companion Wyll is trying to hunt her down in some of his endings. I'm headcanoning he succeeds.
That is indeed unfortunate. In the beginning I thought, Mizora is untouchable, because they had something planned with her in an Avernus DLC or so. But since this is off the table, it would have made sense for Wyll to use the Netherbrain to get revenge on his former pact holder. Poor Wyll, he doesn't even get closure.
"We are all stories in the end. Just make it a good one."