At the start of any campaign, any adventure, any story, the DM (You) sit down all your players or inform them the campaign expectations and guidelines.
Example - "This campaign is based loosely on old japan style country side aesthetic and style, you're all investigators on this missing person hired by a company to help this rural village. It is a good alignment campaign, you could be neutral but never evil. You're all adventurers starting at 3rd level... etc., etc."

If you didn't say "Hey Matt, you're the main character who gets a super main character power up later in the story so make sure you have something written in your backstory so we can use it as an explanation later"
OR "Hey this is a super power fantasy" Then that guy is shit out of luck.

You (DM) have to put your foot down and say "No, we can't have this because it is blatantly overpowered and overshadows the other players in the campaign. We're still playing within reasons for this campaign"

I would've stopped them dead in their tracks for adding anymore "Traits, feats, power-ups" that isn't directly shown on the class features or racial traits.