I for one don't believe she did. From what I gather, she claims that they qualify as disorders because they are not what we evolved "for"
No. They are disorders because they cause deleterious outcomes for those who have those conditions. They present with actual fucking harm experienced by the people who have them. In some cases the negative health issues are fairly obvious (such as with Kallman Syndrome, where there's a significant risk of osteoporosis and a host of other conditions), some are less obvious and largely present as sterility.
You're mixing two topics here. Disorders appear in any number of species, in any number of situations, and are generally based on the deleterious nature of the conditions on the individual with that condition. This is a separate issue from my discussion of the nature of sex.
Sex is an evolved mechanism present in most reproductive species. Some few species do not reproduce sexually, they reproduce via division (bacteria, for example) or via more complex "mating sets" like many algaes. But a huge number of species - especially vertebrates - reproduce sexually. That method of reproduction is the product of evolution. Way, way, wayyyyyyy back hundreds of millions of years ago, our ancestral species evolved so that reproduction occurred as a result of the merging of two different sized gametes. The two gametes have different roles in the creation of offspring, and those gametes place different demands on the bodies that produce them. As a result of those different demands, these species that reproduce via two different sized gametes (called anisogamous species) evolved different anatomical structures and processes. While the anatomies themselves differ from species to species, what is universal is that within any anisogamous species, we can observe that one body type has evolved to support the production of small motile gametes (sperm), and a different body type has evolved to support the production of large sessile gametes (ova).
We have observed that even when the individual does not actually produce gametes, they still conform to one of those two basic anatomical structures. We can also note that no other body type has evolved - there is no other distinct phenotype that has ever been observed within anisogamous species.
We have definitely observed that the growth of those phenotypes can be derailed, can display incomplete or ambiguous development, can even in some very rare cases display a mixture of typically male and typically female elements. But it is also clear in those cases that there are deleterious effects from those developments, often including the inability to reproduce. It's also clear that such conditions aren't within the range of normal range of human development. And it's abundantly clear to anyone without an ideological axe to grind that
these are not evolved phenotypes in and of themselves.
Some people wish to argue that these conditions are either unique sexes of their own, or that they indicate that sex is "bimodal" or "a spectrum". Those arguments are flawed, and demonstrate a considerable lack of understanding of the process of evolution as well as the nature of sexual reproduction across all mammals, all birds, nearly all vertebrates, a huge portion of arthropods, and a whole lot of plants.
Regarding the remainder of your post, I will once again reiterate that evolution has no intent, no objective, it does not select. Evolution is a process, a mechanism. It's a gigantic pachinko machine played out over millions of years.