Indeed this seems like a refutation of the whole thesis that trans athletes are somehow cheating. Intersex conditions are natural (as in no surgery of hormone treatments are involved), yet they confer a competitive advantage - just like genes for bigger lungs or longer limbs confer an advantage to some athletes - so why should a trans person be treated as uniquely advantaged?
The claim isn't that trans athletes are cheating. The claim is they should not be allowed to participate in women's sports.
The intersex athletes support this claim because, although their condition is "natural" in your sense, they are in fact being banned from participation in women's sports. For example, the various individuals mentioned above are restricted from participating in distances from 400m to a mile, including in particular 800m! (Thus they have switched to other distances, but the bans are likely to extend there too.)
