Since they only apply this rule in the events she was most famous for, when other events (like sprints) are more obvious logical locations for it, the IAAF rule seems clearly targeted at her though. That's unfair in itself.
Because she's an almost unique case. Intersex and transgender appear in less than 2% of the population, but far less than 2% of athletes, and each particular condition is quite rare.
The IAAF applied this ruling to particular events because with their association with the IOOC they can't make it a blanket thing.
Ciswomen natural testosterone levels = 0.24-2.4nmol/L
Cismale = 6.9-40nmol/L, average is 12 or so.
Below 6-8nmol/L in young men is considered a medical condition requiring treatment, this varies from country to country.
A ciswoman with a measured level of 5+ nmol/L is considered to have a positive doping test; with twice the highest naturally-occurring amount, it's obvious she had some injections.
Currently, a transwoman who has identified as a woman for a couple of years and whose T is under 10nmol/L is allowed to compete. So there's a gap between ciswomen allowed up to 5, and transwomen allowed 5-10. Transwomen are allowed to have T levels in excess of what would cause concern in a cismale. In other words, transwomen are allowed to have testosterone levels considered normal and healthy for a young cismale.
This intersex athlete falls in that gap. Logically, both intersex and transwomen should be required to have under the same limit as ciswomen, 5nmol/L. However, the IOOC did not choose 5, but 10. Why? Because it actually takes several years for transwomen to reach that level, and some never do. So if they'd chosen 5 it would essentially be a lifetime ban on transwomen, since it's pretty hard to keep up your motivation to train at top level for years and years without competition. But if they choose 10 it's just a couple of years.
The IAAF believes that transwomen and intersex should be held to the same standard as ciswomen, under 5nmol/L. The IOOC, whose considerations are not just fair competition but also inclusivity and image, says 10. Unfortunately for Semenya, she's come between two systems and two standards.
Of course some will argue that exact testosterone levels don't make that much difference, and that's why transwomen are allowed higher levels. But if they don't matter then why can't ciswomen have higher levels? And why do we spend all that money and drama on drug testing?
For fairness, either all women, whether ciswomen, transwomen or intersex, need to have testosterone under 5nmol/L, or they should all be allowed to have it under 10nmol/L. In other words, if we allow transwomen and intersex to have 10, then ciswomen should be allowed to use anabolic steroids up to 10nmol/L.
Fairness in sport, as in other areas, means the same standards are applied to all people.
I would add that this is not about respect for transwomen and transmen or the intersexed. It is about fair competition. In sports you can get a therapeutic use exemption (TEU) for certain drugs, which is why so many swimmers are asthmatics, honest. When a guy's old his testosterone drops, which can lead to loss of muscle mass, erectile dysfunction, frequent illness and depression. This can be treated with testosterone replacement therapy (TRT). Can a Master's Athlete get a TEU for TRT? No, the rules specifically prohibit that. To the master's athlete with low T and general misery who gets TRT, the sporting world says, "we have all respect for you and all sympathy for your medical condition, but you cannot compete."
It can likewise be for transwomen and the intersexed. A single standard - or 5, or 10, or whatever - needs to be applied to all but cismales. Excluding transwomen and the intersexed with testosterone levels above the levels allowed for ciswomen does not mean a lack of respect for transwomen and the intersexed any more than excluding master's athletes on TRT means a lack of respect for older people.
This means some people will miss out on competition. Master's athletes have missed out on competition, transwomen and the intersexed can, too. But competing in sport is not a human right.