> According to the simple scenario, the presence or absence of a Y chromosome is what counts: with it, you are male, and without it, you are female. But doctors have long known that some people straddle the boundary—their sex chromosomes say one thing, but their gonads (ovaries or testes) or sexual anatomy say another. Parents of children with these kinds of conditions—known as intersex conditions, or differences or disorders of sex development (DSDs)—often face difficult decisions about whether to bring up their child as a boy or a girl. Some researchers now say that as many as 1 person in 100 has some form of DSD.
Nor is it only XXY which is the issue:
> For many years, scientists believed that female development was the default programme, and that male development was actively switched on by the presence of a particular gene on the Y chromosome. In 1990, researchers made headlines when they uncovered the identity of this gene, which they called SRY. Just by itself, this gene can switch the gonad from ovarian to testicular development. For example, XX individuals who carry a fragment of the Y chromosome that contains SRY develop as males. ...
> The gonad is not the only source of diversity in sex. A number of DSDs are caused by changes in the machinery that responds to hormonal signals from the gonads and other glands. Complete androgen insensitivity syndrome, or CAIS, for example, arises when a person's cells are deaf to male sex hormones, usually because the receptors that respond to the hormones are not working. People with CAIS have Y chromosomes and internal testes, but their external genitalia are female, and they develop as females at puberty.
Noting "But they are rare—affecting about 1 in 4,500 people." (The "some form of" is for a wide range of issues, like "surgeons reported that they had been operating on a hernia in a man, when they discovered that he had a womb. The man was 70, and had fathered four children.")
Respectfully, you're talking to a scientist, and as such I do have some passing familiarity with "the whole body of literature" or, perhaps more pertinently, the scientific consensus roughly speaking.
The article I shared, while an editorial, is representative of the scientific consensus. Not only that, but it is a reprint of an editorial (a well-referenced, well-cited, well-received and not particularly scientifically controversial one, mind you) which was first published in Nature [1], basically one of the most respected scientific journals: I just don't think it's reasonable for you, without doubt a non-expert, to dismiss it as an "activist" piece of rhetoric. The author is a perfectly respectable science journalist with a PhD in developmental biology, and no particular "activist" agenda. [2]
I don't have any skin in this game: I am a cisgendered heterosexual male, and I honestly don't care either way. I'm just a super curious guy who cares about edge cases, and how society accommodates (or possibly fails to accommodate) these edge cases. I don't know who you are, but you've taken your layman's "common sense" and gone on a mini comment crusade to try to persuade the world that things are simpler than they really are, and I also find that interesting.