This mod "impinge" on NexusMod's rights, it's their private service and they have the right to set conditions on it. One of which, mods cannot remove diversity.
It's as simple as that. The people can go elsewhere to find the same mod or share it among themselves.
Let me guess, you don't have any trans friends. Probably don't have any gay friends, either.
I know no fewer than 5 people who have been physically assaulted over their sexuality or their gender identity. My local pro-LGBTQ church was vandalized by people who left messages about how god hates them.
You deserve all those downvotes you're complaining about if you really believe that non-binary people in the Western world aren't reasonably afraid to express their gender.
And as for "how it relates to..a game". Can you imagine being Jewish and a bunch of pro-nazi mods made it to the frontpage of your favorite game? Can you imagine if then everyone started bitching because the site took those hateful mods down?
Games, as online communities, are used to "innocently" draw people towards extreme beliefs.