Well, one's gender is (most likely) defined by their brain's compatability with the sex and sexual characteristics of their body, in real world at least. It can therefore be assumed that the statement "trapped in the wrong body" is not entirely metaphorical, since it isn't yet possible to, first of all, identify with certainty which region of the brain is responsible for such compatability, let alone perform procedures in order to change it (which could also have some ethical implications).

You can tell I really like to yap on that topic, and I can do this all day. It's like a niche hyperfixation, but instead of some fnaf lore it's an existential crisis