Women with CAIS are born with an XY chromosome pair. Because of the Y chromosome, the women have testes that remain hidden within their groins but they lack neural receptors for androgens so they cannot respond to the androgens that their testes produce. They can, however, respond to the estrogens that their testes produce so they develop physically as women and undergo a feminizing puberty. Since they do not have ovaries or a uterus and do not menstruate they cannot have children. "Women with CAIS have androgen floating around in their brains but no receptors for it to connect to," Wallen says. "Essentially, they have this default female pattern and it's as though they were never exposed to androgen at all."

Source, for those interested.

It is a rarity for this to occur. And I don't think the OP meant to exclude cases like this. It is just rare, so it wasn't included. Women with xy chromosomes develop like women with xx chromosomes. The OP mentioned stuff about people believing in a 3rd chromosome that was somehow a different sex or showing that there are "a plurality of genders". But it just isn't true, which is what I believe the OP was trying to get across. So I don't think your friend's case is what the OP was referring to.

Just for the record, I couldn't care less about someone's chromosomes and if I make a mistake and they ask me to call them by their preferred pronoun, I absolutely will, without question. Sometimes you just can't be sure--it happens. But in your friend's case, that isn't an issue, since she developed like other biologically-female people.