This is a tough question. I really do feel for the women Semenya steamrolled. They claimed it wasn't fair. It wasn't.
See, an Olympic gold is about a lot of things: hard work, an incredible performance, the biggest stage, and, YES, genetic advantages.
Before you tune out, I am not saying that being born a man in a woman's body de facto means that you get to be a dude, beat the girls, and get the gold . . .
Here is my short answer: there is a difference between sex and gender. Sex is genetic. If you have XY chromosomes, then you are genetically male, usually. Gender is different -- and not just because of the clothes you wear or the length which your parents cut your hair or whether you wore pink or blue as a baby. Gender is a social construct that is important in determining perceived sex.
That wasn't so crazy, was it? But if you're still with me, then you are either still unconvinced or you were already convinced.
So, here's the elaboration: [Don't worry, I'll include links below; quoted stuff in links.] About "1 in 15,000" people are born intersex. "These athletes have a genetic condition where the testosterone receptor has a mutation which means they are unable to obtain any benefit from it (or from injected testosterone)." "[T]hey have male hormones, but those hormones cannot act because of a mutation in the protein to which they are supposed to bind. They would look and behave like a girl, . . . [m]any models and film stars have this disorder."
Okay, so the idea is that, intersex women are different from non-intersex women, but the difference should not matter in practice for athletics.
"Apart from the fact that they can't bear children, they are completely female." Yet these women have XY chromosomes. If sex testing were limited to chromosomes, they would be declared male."
They cannot bear children, which might be a bummer for them, but irrelevant to our conversation.
But that's not the only possibility: "At the other end of the spectrum are those who . . . should be female, but have too much action from male hormones, because of a deficiency of the stress hormone, cortisol. Somebody with this condition, called congenital adrenal hyperplasia may look on the outside like a boy, but once a month they may have blood in their urine. The genitalia doesn't need to be completely male, it can be somewhere in between. These days, doctors would do genital corrective surgery quite early on."
This all blurs the line between genetic advantage and misplaced gender, I admit, but is this her fault?
If she is to blame for producing too little or too much of a hormone --naturally -- then where does genetic advantage end and cheating, doping, or gender begin?
https://www.theguardian.com/world/2009/aug/20/what-sex-is-caster-semenya
https://www.theguardian.com/sport/2016/aug/22/semenyas-gold-is-being-tarnished-by-hormone-row
Sources ^
I do not necessarily agree with everything I wrote above, but I feel bad for the girl and all of the controversy she has had to deal with for years. I also acknowledge that this is a tough issue that may take decades to solve.
(Also, I admit, she looks more like a man than the other girls; all that I think that means is that she is in the other, second, camp of women who look like men because of a cortisol deficiency. If she has this naturally, then that's about as unfair as having long arms or a crazy VO2 max.)