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If someone's body has the typical properties for males or females, it's generally considered as such. If someone was born with properties of both, they maybe considered intersex. Trans people often don't fit very well into this system. A trans woman for example may have XY genes (a typically male trait) but estrogen and a vagina (typically female traits).
Male and female work well for most people, but there are some people whose bodies aren't strictly male or female. For those people, medicine generally has to individually consider the relevant traits.
It's really fascinating stuff, and way more complex than they teach us in school. Hopefully, this is changing though. With how important survival is to evolution and how prevalent this stuff seems to be, I can't imagine that there isn't some reason that a species would have so many variations. I wonder how common it is for other species to have variations that aren't simply the xx and xy equivalent in nature. I wonder if it is possible for there to be a 3rd chromosome type in any other species. It's so cool that this is all something that is getting more and more awareness.
That is insanely amazing!