As people have said before, it's because they made some jokes on twitter. They probably shouldn't have done that but they did. That was enough to have them deemed transphobic and that's not a label you are allowed to shake off so all subsequent actions must be viewed through that lens. Sure, it may seem like being the first company to produce a AAA game with trans options is a good thing and something that demonstrates support for the trans community - but we already know they are transphobic so we need to understand these options in terms of them being transphobic. So you just work backwards from there and there is always a way you can argue it if you really want to.
And of course the problem is that it doesn't matter what CDPR do now. If they apologise for the jokes, if they offer more trans options and characters, if they hire more trans employees. All these things will be either argued to be transphobic somehow or dismissed as cheap pandering to get money. They need to shut down and start up again with assumed names. Other than that, they may as well not bother doing anything in future because nothing will be enough, if all they care about is pleasing Resetera. Hopefully though, they can see the bigger picture and will continue to include trans options and characters in their games, despite this being vilified by the Resetera people.