I think if Toby really is going to do the "your party member is a boss in weird route" thing then Ralsei would be way more thematically appropriate to be the final boss. I imagine it'd be like Undyne/Sans where we first get to fight Susie, but she'd be a roadblock at best, while Ralsei will wait for us at the final fountain in Castle Town, hoping 'til the very end that we'll change, and being an insane challenge spike if we proceed.