How is intersex not a disorder when there is something wrong with the way their chromosomes, and genitals are? How do you define a disorder that intersex doesn't count as a disorder?

Not all DSDs involve atypical sex chromosomes, though most involve a genetic mutation of some kind. Many people have genetic mutations that can cause or contribute to disease and disorders - I know of several that I have personally - but not all people with these mutations develop disease or disorders. Oxford defines a disorder as

an illness or condition that disrupts normal physical or mental functions

But even some illnesses and conditions that once were considered disorders per this description are not seen that way today coz the treatments for them are simple and 100% effective.

For example, I have an inherited, presumably genetic condition called pernicious anemia, that if untreated leads invariably to death - a long, slow and painful death, and which prior to getting to the terminal stage causes people with PA to lose their minds. But with a monthly IM injection of vitamin B-12, which is cheap and easy to self-administer, pernicious anemia is 100% reversed/cured. So most of us with pernicious anemia do not see it as a disorder, nor do our physicians.

Now that genome sequencing is being done for more and more people, it's turning out that genetic mutations that are linked to disease and disorders, but are not always causative of them in every case, are more common than previously assumed:

https://www.sciencemag.org/news/2017/06/one-five-healthy-adults-may-carry-disease-related-genetic-mutations

How is intersex not a disorder when there is something wrong with the way their chromosomes, and genitals are?

You keep revealing that you actually know very little about DSDs. Not all DSDs affect the genitals. Many people with DSDs have typical-looking genitals and/or normally functioning gonads.

Please when you speak of these matters don't use language and framing that lump the two sexes together and make the mistake of assuming that what's true of human males is also true of human females. Only the male gonads, the testes, are considered part of the genitals. Human female gonads, the ovaries, are not external and thus not usually called genitals like the testes are. Whereas testes are between human males' legs, human ovaries are internal organs inside the abdomen at considerable distance from our crotch and genitals, eg our vulvas.

One of the most common conditions that in the past was labelled "intersex" or a DSD is micro-penis, which is a normally functioning male genital organ that is smaller than normal but which functions normally. Most micro-penises and normally developed and function fine; they're just small. Another condition traditionally considered "intersex" and a DSD is hypospadias, a congenital condition where the male urethra opens on the underside of the penis. This doesn't impair a male person's ability to urinate or ejaculate seminal fluid - it just looks odd. And it's easily corrected by surgery.

By far the single most common DSD is congenital adrenal hyperplasia, CAH, which I've read accounts for the majority of ALL DSDs (though I can't find the source at the moment). CAH comes in several different forms - and only the rarest form, known as classical CAH, which can be fatal if it involves salt-wasting, requires treatment and might affects genitals. Yet even classical CAH usually only affects the appearance of female genitals Most males with CAH have normal-looking and functioning genitals. The most common form of CAH is the mild form. Many persons with the mild form have no obvious symptoms.

https://rarediseases.org/rare-diseases/congenital-adrenal-hyperplasia/