Why should we let the cats choose their own mates when the player can manually set mates? Why should we let the mentors be assigned apprentices automatically when the player can manually assign apprentices? Why should we let the deputy be chosen automatically when the player can manually promote a deputy? Why should we include any RNG elements when we already include options for the player to manually make those decisions. I don't understand why you're only asking this question in regards to the trans cats. Sounds like you only take issue with one thing, and that reflects badly on you.
Those are all natural things that can happen in a clan. I understand those elements being randomized, but not their genders. Gender is a personable thing, that each person has a unique take on, depending on who who are. There's some that believe there's only two, while others believe there's multiple. Sex doesn't equal gender, so why are the cats referred to as male and female instead of tom and she-cat like in the books? Why are male and female the gender identities if they aren't genders? If the game has genders, why can't you set the pronouns of your cats?
Why does gender even matter to cats anyway? It's nice that gender diverse people can headcanon their original cat characters as gender diverse, but why would a cat want to be nonbinary or a trans male/female if the issues with gender and gender identity stems from human socialization and stereotypes of male and female people of the man and woman gender?
Pronouns are actually an upcoming update. As you can imagine, making sure all the text in the game can dynamically update to given pronouns of specific cats is rather complex, which is why a neutral they/them was used originally. But, regardless, we could argue this all day and likely get no where. The bottom line is that this is the decision that has been made by the contributor team and is very very very unlikely to ever change. You do not have to play the game if it makes you uncomfortable and you can always change the gender of the cat if it displeases you.