Considering how many trans (and LGBT in general) rights stages are still up, this seems to be a case of one mod with (putting it lightly) a twisted definition of what is a political statement, and who happened to be the one to deliver the bad verdict on the reports against this stage by transphobic players.
That said, Nintendo should definitely make sure their internal policy prevents mods from making bad decisions like this on human rights topics, but there is evidence to the contrary that the company is not a blatantly anti-trans monster (Splatoon, Miiverse), where they let pro-trans user-generated content fly.
That said, Nintendo should definitely make sure their internal policy prevents mods from making bad decisions like this on human rights topics, but there is evidence to the contrary that the company is not a blatantly anti-trans monster (Splatoon, Miiverse), where they let pro-trans user-generated content fly.