The IAAF is being as politic & cagey as possible - so no, they've not said in so many words that Semenya has a male DSD, not a female DSD.
The IAAF is respecting Semenya's right to identify as a woman, & to be legally recognized as a woman. Still, when the May CAS ruling was announced & there was such a hue & cry about Semenya having to lower testosterone in order to continue to compete in certain women's events, the IAAF did say Semenya can always run in men's events.
In May, the World Medical Association, at the request of the South African Medical Association, announced it had told physicians not to comply with the IAAF regs re Semenya & other XY DSD athletes with the same characteristics. In reply, the IAAF published a statement pointing out that in most of the world, longstanding first-line treatment for XY DSD patients with female gender identity who decide they want to hold onto that identity is to have their male gonads surgically removed. This not only eliminates the source of the high T that masculinizes (& typically distresses) such patients, it also removes the high risk of testicular cancer that many of them have.
Reading between the lines of the IAAF reply (see below), they seemed to to be implicitly trying to raise some salient questions. Such as:
Why would anyone who truly considers themselves to be female be so insistent on keeping their testes?
In an era when even ultra-feminine women like Angelina Jolie & Christina Applegate are willing to get their breasts completely cut off to lower their inherited risk of cancer, why would someone who self-describes as an "all natural woman" refuse to even consider removing male gonads that could well be malignant? (Surgery, after all, is thousands of years old not a new, experimental & "unnatural" practice; & athletes get surgery done all the time.)
Why is the IAAF's alternative suggestion that Semenya could easily lower her T to acceptable levels by simply taking female birth control pills being so roundly rejected & denounced as unfair & discriminatory to Semenya when females (including athletes) everywhere in the world take, & are expected to take, those same birth control pills as a matter of course?
Why are female contraceptive pills anathema to Semenya when in the medical community & amongst the public alike nowadays these very medications are seen as the most "gender-affirming" gold-standard of care for XY persons with female gender IDs?