Was Rafaed playing 7D chess this entire time, hoping to get a shot at defeating Mikaros and "The Will of the World" itself?
This would explain why he did not let Alicia go Berserk back when they met Helck, he did not actually want him to despair.
This definitely feels like an Atlus game with final bosses that can reflect physical attacks, are immune to magic, and/or can use gigamagic spells that can alter reality itself; and a main character that is mainly built around physical attacks.