I'm curious what uses you have in mind--anything that's an online competitive (i.e., you compete against other players--doesn't need to be esports sweaty) game I don't think there's a strong case for allowing injected code, since that's an avenue for gaining an unfair advantage and thereby worsening other players' enjoyment, and anything offline I can't see it being worth a company's time and money to prosecute.
This. Nintendo is one of the least ethical videogame companies out there. Even when they come up with something new and innovative, it's so locked down you're better off waiting to play someone else's copycat of it.
I think the problem is that the ruling now establishes that overlays and injected code are a copyright violation. Therefor any overlay or injected code is now illegal unless you have permission from the authors if the game.