Im confused, is she a girl or a guy, why does the dad call her son? Did she become a boy a...

the dad doesn't wanna call her a girl and since spirits r generally genderless or smth it's surprising that she even has a gender

I think that she doesn’t have a gender physically , but when she got transported to “earth” she became a girl physically to fit in since there is no naturally physically gender less people. But when she came back, she went back to her gender less self but she identifies as a girl now. I think her father calls her son because she looks more like a man.

Exactly. The main protagonist grew up as a girl, but since she is originally genderless in her own world like her Father, her dad prefers to call her a son. It's like, in human standards and english language, one is generally called a man as a neutral-gender noun.