all three of the medalists in the 800m had the same 46,XY karyotype DSD condition

I don't know what you mean by "the same 45, XY karyotype DSD condition" here. Karyotype means "the number and visual appearance of the chromosomes in the cell nuclei of an organism or species" (Oxford).

Semenya almost certainly has 5-ARD, an enzyme deficiency caused by a genetic mutation that in males affects development of sex organs in utero & thus is a DSD. Genes, and gene mutations, are found on chromosomes, but they do not affect the number and visual appearance of a person's chromosomes.

The other medalists in the women's 800m at the 2016 Olympics - Niyonsaba & Wambui - have said they are subject to WA's current rules for XY DSD athletes just as Semenya is coz they too have conditions that cause them to have "high testosterone" like Semenya does. Which is code for saying they too are XY with testes, male levels of T & male typical sensitivity to T (in other words, they don't have CAIS).

However, Niyonsaba & Wambui have not revealed exactly which specific XY DSDs they have - just as Semenya hasn't. We only know that Semenya's DSD is XY 5-ARD because documents of the legal proceedings have been released by the CAS, & 5-ARD is the one condition that both sides focused on.

Niyonsaba & Wambui could also have XY 5-ARD, or they could have another XY DSD that affects males very similarly, such as 17-beta-hydroxysteroid dehydrogenase 3 deficiency.

That condition is supremely rarer than being transgender and displaced all female athletes that year

The kinds of XY DSDs that athletes like Semenya, Niyonsaba & Wambui have are indeed extremely rare in the general population. But in elite level women's international sports, such conditions are 140 times more common than in the general population. Which means that in elite international women's sports, there have been & still are many, many more XY DSDs athletes than males who identify as "trans."

BTW, Niyonsaba will be competing in the women's 5000m in Tokyo. Semenya is still trying to qualify for that event, but probably won't make it. Under the current rules, XY DSD athletes can compete in women's sprints and long distance events without reducing their T. T-reduction is only required if they want to compete in middle-distance events.

Meanwhile Margaret Wambui has recently publicly called for a new sports division for athletes with DSDs. Wambui really meant a division for athletes with XY DSDs, testes, male levels of T & male sensitivity to T - but he didn't say so coz of the fiction that the problem in women's sports is with DSDs generally, not with DSDs that only occur in males.

Still, Wambui deserves props for being the first XY DSD athlete I've heard of who has acknowledged, albeit indirectly, that XY persons with DSDs don't belong in women's sports. Semenya is still pressing the case that his "identity" should trump his sex, spouting lies like "I am a woman, and I am strong" & claiming that the reason many people object to Semenya competing in women's sports is not because Semenya is male, but because "I am the best, and when you are the best other people try to destroy you."