Unfortunately by now we heard more about what is planned as costumization instead of the story, so I don’t exactly see how in this case this is relevant. Especially since you are acting like stories that are including people of different races/sexualities/genders would either not be “actual stories” or just not interesting for you…
I’m sorry but I will be honest here: Where do you get the impression that this options will lead to major rewrittes when we in fact didn’t even see one written word of the game? By now I have seen much enthusiasm but with not much planning behind it, I have seen enthusiasm, but only as long as the potential players don’t come up with reasonable complaints, I have seen enthusiasm from both the community and the author for his project, but I still didn’t see one thing about the game itself. And by now it starts to get ridiculous…
Tripel A games are no comparison, alone because choices and writing alone are not that important but also game mechanics and the visual implementation for those which indeed would make a game more work with costumization. But we are talking choice script here. Nobody forces the author to go into great detail about outfits and visuals. Many games let things vague. Freak: Amidst the neon lights gives a bunch of costumization with influences on character reaction, but stays always vague enough so that the question for pants or dresses isn’t even needed (but it explicitely gives the option to define the gender of the MC by the way…), so it is possible to give various options without ending up to go into the details.