For reasons (I work for one company, but our work is for both ourselves and sometimes in partnership with others), I often end up with two (or more) instances of certain sites and apps (like two organizational Gitlab instances). To make my life easier, I pick one to be dark and one to be light by default so I can tell at a glance "Ah, this is my corp version, and this other is for some customer". My system also uses automatic dark/light switching.
If I'm setting this up during the day, when I normally work, those external sites would easily end up with the "auto" behavior by this very poor design in the blog, when that is not my actual intent. This would result in me having to set it twice (the second time in the evening) to have my desired behavior which is a nuisance. The explicit option is better here, not whatever this silliness is in the article. [0]
At least I've read this article so sites and apps using this stupid option wouldn't be too big of a surprise to me, I'd hate to have to explain this to other people who haven't read it though. Principle of least surprise is a good thing, not something to deliberately work against like this author wants.
EDIT:
[0] Actually, this demonstrates a crucial flaw in the system's design. If I want to set the current default as the permanent setting, I have to wait until a particular time of day to do so. That's even worse than I'd previously realized. You can only set permanent light in the evening (or by changing your OS/browser settings, changing the site, and then changing OS/browser back). You can only set permanent dark during the day (without that same stupid exercise).
This is a terrible design concept.
But this means you're "abusing" dark/light mode to signal unrelated information. If some visual customization (theme, font size, etc.) happens to allow you to do something like that, then of course more power to you, but I don't think it has any relevance to the design of the thing itself. It just seems unreasonable to me to expect designers to consider all the ways their designs could do double-duty for any given user (cf. "every change breaks someone's workflow").