I'm really not certain that's the idea, and it certainly does not feel very charitable. Perhaps you are holding on a little too tightly to this high vs. low level distinction (the simple mental model being attacked)? I compared the author's argument to a reductio. A reductio is not intentionally misleading?
This paper reminds me of "It's Time for Operating Systems to Rediscover Hardware". See: https://www.youtube.com/watch?v=36myc8wQhLo
There, an argument is made that our simple model of "the machine" is also wrong. There, the speaker points out much of the software that is running on our complex SoCs, with multiple cores, is firmware. To which, I'd imagine you might argue: "But that firmware is not the OS?! This talk is misleading!"
> If the author knew this, and his central premise were that no low-level programming language existed anymore, the article would be titled differently and he wouldn't be making the arguments against C specifically.
I am not sure. I believe the reason C is targeted specifically is because C communities are where this myth, and its religiosity (!), is the strongest.
> But this is essentially packaged as clickbait
I'd agree that the article is provocative, but it would seem to have good reason to be. Lots and lots of people think both C and our processors must work one way. That there is or was some level of naturalism/determinism at play. The author is simply pointing out -- not so much.
> After writing out my charitable interpretation of the author's capabilities, this interpretation only leaves me more disgusted with the article as a writing output.
Yes, it was designed to make you mad. But if you were forced to write a rebuttal to the entire article, from a charitable POV, I think you'd see there is some value to the reader in realizing this tight coupling (C and processor design) is not a necessary condition.