The real issue with hypertapping isn't that "not everyone can do it," really. It's the question of if it crosses the line into being inherently injurious to the player in the medium or even short term, in which case the advantage doesn't come from either natural or learned skill but a willingness to ruin your hands for silly game points.
Generally speaking regulated sports tend to draw lines here too, though obviously some draw them fairly far into the injury territory. Most of those are explicitly fighting sports though.
At least two of the best Starcraft 2 players, Maru and Byun, are having serious wrist issues. SC2 doesn't involve tricks like the ones mentioned in the article, and still actions per minute (APM) matter a lot and people get hurt. I've never heard anyone proposing regulations over APM.
OTOH, almost every sport hurts at pro level, and I think it's safe to say that all pro sports are unhealthy, except a few of them. E.g. Federer has serious issues with his knees, has had more injuries than an average 60 year old man.
I don't disagree that most sports are bad for the body at pro levels, but even so generally speaking they usually have implicit or explicit rules against deliberate short term damage to help you win.
The most obvious is really that while the case for rules against performance enhancing drugs is usually that they just give an unfair advantage, if you look at what's actually banned and what's not, and how natural advantages are treated, it seems pretty clear that most banned substances are also the most harmful, while others skate under regulation. Esports hasn't even reckoned with this yet afaik, even at pro levels. We'll see where we're at in 10-20 years as it mainstreams.
As you point out in the other branch, that's kind of motivated largely by PR concerns. People are mostly ok with basically anyone ruining their body slowly for a job (unless it's their own), but they balk at rapid injury. My point is really just that hypertapping potentially gets very close to this line, and that's a big part of why there was a drive to find a replacement technique or even ban it from competitive use.
Anyways, there's a lot more research into how to do high APMs with a keyboard and mouse ergonomically than there is with an NES controller, which also has a hard and shallow throw compared to either of those and a very unergonomic shape to begin with. There's a lot of reasons they aren't obviously comparable to each other when talking about the RSIs they can cause.
Gymnastics is also good example. Some routines are just banned, because there is possibility of damage or too high risks. And it is quite fair as long as it is clear upfront and everyone follows the same rules.
That regulations are more in the line "we don't want participants to die or get crippled on live TV". Because gimnastics are absolutely insane for your body, the number of people who end up with totally destroyed knees, shoulders, ankles... before their 30's is horrifying.
Generally speaking regulated sports tend to draw lines here too, though obviously some draw them fairly far into the injury territory. Most of those are explicitly fighting sports though.