I think this is kind of a mixed message here. Minorities are discriminate against or downright persecuted because of them being different.
When we have the "duplos", a very small minority of true hermaphrodites, being hated and feared because they are dissimilar from the perceived (by some) norm i believe it becomes hard not to draw paralels with what happens in real life with trans people.
The important part is that people pretty much always get descriminated for
perceived differences. This is not exclusive to trans people, because every in-group has perceptions about out-groups for any reasons you could think of. That's just how bigotry works in every case. In fact I could probably think of several minorities that fit this game's duplo allegory better than trans people.
Duplos are obviously not very different, when there's characters like Zoey and Fiona, who aren't any less horny than Ashe, or characters like Kate, who are ashamed of their kinks, or actual predators like Natasha. Think of the implications. Is it bad to be horny and to have kinks (as long as everything is consensual), just because that's how duplos get perceived?
This game is less about an irl minorities analog and more about Ashe accepting herself for who she is (which is actually a fantastically executed part). You know, like "What if people hate me, because I'm horny/kinky/hot for my sister?" The bigotry in the game world is just the mechanism that triggers Ashe's self-doubt. But the real katharsis wouldn't be about accepting duplos despite the perceived differences, but about letting everybody be horny and kinky, whether they're duplo or not.