So the Nidoran-male can't have a vagina but can identify as female, is that what you're saying? Just trying to make sure I understand completely.

well yes because nidoran male and female are the same species … this question is like asking “so the male pikachu can’t have a vagina but can identify as a female, is that what you’re saying?” not trying to be snarky at all either, just trying to compare it for you so you see what I mean

in the games, nidoran male/female produce offspring that are either nidoran male or female! nidoran female’s babies can be either sex, so they’re the same species (this is the case with illumise and volbeat as well, making them the “same species” but split into 2 pokemon in the game)

your pokemon may identify however it wishes

also i realized i read the last one backwards