That was the usual strangeness, but it doesn't make Mashirou look very good...
While it's a trope in hero shows like Kamen Rider that the protagonist gets their powers from the Evil Organization, I can't think of any examples that being the case in magical girl shows.
Except for Puella Magi Madoka,
spoiler
where the cute mascots are the Evil Masterminds, but that show's a deconstruction of the genre.
Chrome does act more like a hero than an Evil Mastermind, and doesn't even need Fossa Magna to do what he does...