Depends on if you're primarily interested in getting utility as soon as possible, in which case use whatever solves the problem you'd most like to solve. If that is making some web app, that'd be Javascript.
If you're interested in learning programming well for its own sake, probably check out "How to Design Programs" by Felleisen et al., or "Structure and Interpretation of Computer Programs" by Abelson et al.
"Therefore... what? Just give up? Or start over from a non-flawed base?" - those would both be ways to avoid the presumed local optima, yes.
"Which is what? Still to be created, or does it exist?" - several different 'initial stakes'/bases in the space of programming languages exist/were made/can be created than the family of languages mentioned in OP. Exploration from those might yield better optima. The widespread adoption of the current industry 'standard' languages seems an accident of history, not guided by quality of language.
"Are the bases flawed because they are low level?" - yes. A significant part of the computing field is about abstractions. Improving the level of the technology is one of the arguments the article here makes too. Besides, it's the implicit admission of everyone who doesn't advocate/write assembly.
"The encouraging thing today is that we're kind of converging on good practices in language design." - doubtful that we'll arrive at good practices in language design through incremental steps from a flawed base. All the mentioned languages are low-level.
The site implies assembly is how computers really work. IMO, assembly is just an incidental implementation detail of little note. High level language chips are possible, after all.
Solve problems!
Caveat: Many books seem to have bad problems. If the majority of the problems seem to be the same problem with different parameters, that might raise a warning.
To quote Hamming:
"""In science if you know what you are doing you should not be doing it.
In engineering if you do not know what you are doing you should not be doing it."""
It follows that regurgitating answers to already solved problems is good engineering :)
For one, relying on information to surface in light-weight form means that - even if it surfaced - you would be behind the curve.
Secondly, it probably doesn't surface. A heavy book you engage with builds rich models: you don't get that from light-weight online content.
Thirdly, if you want to positively differentiate yourself, acquiring information others don't have is one method. Reading books others don't read is one way to get that information.
Anecdote: Feynman used to have others ask him to look at the integrals they'd been unable to solve, and he was often able to solve them - something he attributes to having read a different math book that presented some seldom-presented integration technique.