As the expert on this, RunRagged, can confirm, Semenya has no female reproductive organs and lacks mammary glands as well. No anatomical features unique to XX females are present. So nobody is saying, "This woman with breasts and various female body parts is actually male." But various posters ARE saying, "This individual who has all male anatomy minus one very immediately noticeable part, and more importantly, male hormone levels both during competition and during development, is male."
Agree or not, that is what various posters contend. Now, the prostate missing was added by RunRagged - and many thanks to her for very informed and educated posting - so perhaps more than just one organ is absent when compared to a great majority of males.
But neither the prostate nor the other appendage is what gives the best male runners an 11% advantage over the best female runners over a wide range of distances. (It could be 10%, then 9, as the events get longer. By the way, you may notice that Semenya was nowhere near 11% better than the best XX athletes. That would have put the performances in question close to men's world records. But Semenya is also not at the very top of male performance. Nor are 99.99% of male athletes.)
Testosterone and other hormones do. Semenya's hormones are, and have been since prior to birth, well within (not at the bottom end of) typical male ranges.
This is why many believe that Semenya, athough welcome to compete in men's competitions, should not be allowed to compete in women's competitions. You may agree or not, but that is what one faction of posters believes. Just clearing up apparent confusion as to what exactly is being written here.