A patent says you own the thing, but you can license other companies to use it. Even if all the big companies are in it together, Kogado Studio would most likely want to cash in on the licensing agreements that patent holds and Atlus would NOT want to pay Nintendo for something they did first.

The first 2 who would be able to argue they should own said patent is Kogado Studio who made Cosmic Soldier (1985, but could not get it since they classified the monsters as "aliens") or Atlus with Digital Devil Story: Megami Tensei (1987, monsters have been known as demons, shadows, and monsters).

The way I see it, Nintendo's patent change mid lawsuit about ride mechanics was seen unfavorably. Patents they're using against Palworld were filed in 2024 after it came out. Plus, it doesn't change the fact that Atlus or Kogado Studio can come in and demand patent ownership, show proof, and win.