Again -- I think your impression is the result of the contentious tone of the article. Yes, the article explicitly states:
"Think of programming languages as belonging on a continuum, with assembly at one end and the interface to the Starship Enterprise’s computer at the other. Low-level languages are “close to the metal,” whereas high-level languages are closer to how humans think."
But then spends the rest of the article debunking this commonly held notion, specifically and explicitly re: C, but also implicitly re: assembly.See the very next section "FAST PDP-11 EMULATORS"
"The root cause of the Spectre and Meltdown vulnerabilities was that processor architects were trying to build not just fast processors, but fast processors that expose the same abstract machine as a PDP-11. This is essential because it allows C programmers to continue in the belief that their language is close to the underlying hardware."
The author obviously knows that assembly suffers from the same abstraction penalty. The author is saying, because C and processor design has been so tightly intertwined, we cannot program "close to the metal" because "the machine" is actually a very fast PDP-11 emulator.See also the section "IMAGINING A NON-C PROCESSOR", where the author explicitly discusses alternative processor designs (which would of course require new assembly languages!).
The author is actually trying something like a reductio on your mental model. When the author states "Think of programming languages as belonging on a continuum", the author is really saying "This is everyone's impression, but ... when you look a little deeper you see the cracks (which are actually contradictions)."