it seems to me like it’s about someone whose gender or gender presentation doesn’t line up with the typical binary. “you’ve got your mother in a whirl, she’s not sure if you’re a boy or a girl” as well as “you wanna be there when they count up the dudes” and “you’ve torn your dress”. maybe they’re non-binary or gender fluid, tho i doubt Bowie would’ve had those words in mind when he wrote the song.
the song also makes a soft reference to Bowie’s bisexuality, with “you like me, and i like it all”, saying he likes the subject in all their non-traditional gender.
a big part of the theme is how most people seem not to understand the subject— their mother is confused by them, and as Bowie says, “they put you down, they say i’m wrong”... but Bowie sings as a lover, and he loves the subject, calamity’s child, for all they are, as everything they are.