Women with DSD on averave have a higher testosterone level. Testosterone generally makes you better at sports. The Olympics select for the very best athletes.
In other words: the Olympics are selecting for women with DSD, so once you start doing 100% testing you'll find an incidence far above that of the general population.
There are proofs that male chromosomes are beneficial for example in boxing for women, but it’s not because of testosterone as far as we know. In almost every other sport, it’s not beneficial at all, and even negative because of the mentioned testosterone insensitivity.
Talent scouts specifically sought out males like Semenya who were erroneously registered as female at birth, knowing that their male physical advantage would give them an edge in women's competitions.
The specific condition he has (5-alpha reductase deficiency) is one that only affects males, conferring upon them internal testicles and a micropenis. But male development, including all the testosterone-driven advantages that distinguish male and female athletic performance, is otherwise normal.
His gold medal in the 2016 Rio Olympics women's 800m, along with silver and bronze being taken by two other males with similar conditions, is the reason why World Athletics (then the IAAF) and, later, the IOC started to move policy away from eligibility by identity documentation to empirical testing of sex advantage.
The policy change discussed in the linked article wouldn't have happened without athletes like Semenya taking advantage of the previous flawed policy, to the detriment of female athletes.
And of course he would have gone through male puberty, not female puberty. This would have been obvious then, and the result of this is obvious now if you see him in interviews. Male-typical build, male-typical vocal tone. Even his now-wife assumed (correctly) that he is male when she first met him.
Semenya has to double down on this narrative that he is a woman otherwise he will have to admit that his successful sporting career as a woman will have been a lie.
In fact, I'm not aware of any genetic testing program ever catching any deliberate cheating, only people who were raised from birth as women. The very first example of this, (1), Dora/Heinrich Ratjen (2) seems to have been an intersex person who was definitely raised as a girl from birth who was a bit confused about what their body was doing. But all the way back in the 1950's when their 1936 Olympics became a big deal, we have lurid tales in the English language media of deliberate cheating that don't seem to have been supported by anything that Ratjen ever did.
1: http://linuxmafia.com/faq/Essays/marriage.html 2: https://en.wikipedia.org/wiki/Heinrich_Ratjen
How else should the person who just got that information interpret it except... Sorry, you're not really deserving, even though your score qualifies you. And what do call someone who has a score that qualifies but doesn't get to go?
And there are far more of people with this experience than the experience of being born and treated by society as a man and becoming an Olympic athlete as a woman.