XX and XY have a strong correlation with sex traits, but not a 1:1 correspondence. (And neither those chromosome configurations nor other biological sex traits map 1:1 to external genitalia, which is Italy the basis of socially ascribed gender.)

So the fact that XX and XY configurations exist and other configurations are considered "defects" doesn't make biological sex a binary trait that correspondence to the manner in which gender is usually digitally ascribed and for which people are labeled "transgender" when their gender identity differs from that social judgement.