from my undertanding, and after having triggerd specific dialog options on the "good ending" route, I think they are more queer gender than anything. whether as a trauma response or due to what being a "woman" means for the enviroment they were raised in, it seemed like they kind of felt some sort of disconnection to it.
In game, the only character I've noticed using any pronouns when talking about them is Ronin, who specifically only uses "they/ them" whit Ther, but since the creator has referd to them as a "she", then we can safely assume both ways are okay¿