I quite enjoyed reading those excerpts you provided on the distinction between sci-fi and fantasy. But I disagreed with much of it.
In an analytic mood, it might be wondered why some folks favor one of these genres over the other. One possibility has to do with a predilection towards naturalism and/or atheism vs. supernaturalism and/or theism. That is: sci-fi (even if it’s “soft” or wildly speculative) has a naturalistic orientation. In contrast, fantasy tends to embrace the supernatural, the paranormal, magic or quasi-religious signifiers.
Yeah, I'd say there's a fantasy element to Batman as well, particularly as he's depicted in the comics. (For obvious reasons, however, this is significantly lesser than that of his superhuman contemporaries.) I'm also a bit curious as to where the writer of said piece, a science-fiction author of some renown w/ over 60 published novels to his credit, stands on other related concepts like time travel. All the same, he does make some valid arguments worthy of consideration. Case in point, Superman is quite literally the product of imagination. The mere notion of a man soaring through the heavens by sheer force of will is unquestionably the stuff of dreams, and whatever fake or specious science is later applied to that so as to give it some light measure of credibility simply doesn't negate the fact. Indeed, it's largely due to this emphasis on fantasy that the paper-thin disguise trope works so well IMO.
From tvtropes.org:
Paper-Thin Disguise
"A character that the other characters should recognize (or at least recognize as out of place) dons a disguise and is treated as neither recognizable nor conspicuous. This disguise is so completely transparent that the audience wants to shout "For the love of God, it's him!"
The external reason for the flimsy disguise may be that the creators want to signal the presence of a disguise to the audience before the other characters catch on (a sort of Reverse Whodunnit). Sometimes, the character may also be a Special Guest the director wants to get their money out of. All the same, you often get The Reveal staged in such a way to make it clear that the director really thought you wouldn't have worked it out by now. For the more perceptive viewers, it's a case of The Un-Twist.
While not a Dead Horse Trope, these days Paper Thin Disguises are parodied as often as they are used seriously. Many Stock Parody Jokes involve a person appearing who coincidentally looks just like the person wearing a bad disguise, usually seen in cartoons.
The trope is still an important dramatic convention in live theater and opera productions — where a really good disguise would render the character unidentifiable from the cheap seats, and be beyond the scope of the prop budget to boot — but is usually employed along with some kind of nod to audience acknowledging the absurdity. This can sometimes be exaggerated for comedic effect, for example wearing bunny ears and becoming indistinguishable from a real rabbit, or pretending to be an ancient statue by simply standing still in a specific pose. Children's shows still employ this trope regularly without any parody element.
This trope differs from the general case of Wig, Dress, Accent in that a Wig, Dress, Accent disguise is always plausible. Paper Thin Disguise also includes the element of being staged as if the disguise really is convincing, which is not generally present in Wig, Dress, Accent."
That said, I have no real beef with calling Superman “fantasy” and (say) Batman “sci-fi.” But to the extent that such genre classifications are valid, so too (IMO) are the sub-genre distinctions. For example, Superman and Captain Marvel/Shazam are virtually identical in terms of their fanciful superpowers (so much so that DC successfully sued Fawcett for copyright infringement). Therefore, put both in the same fantasy category...? Except… one character is explained using a “science” pretext and the other via a wizard who channels gods and magic. This difference, I would argue, warrants at least some acknowledgment and makes separate labels/terminology useful.
While it's true to say that pretext matters, the science in Superman's origin is so "soft" that it's closer to magic in terms of how general audiences largely perceive it. And in virtually all other areas, the character isn't terribly different from (say) Thor, Captain Marvel/Shazam or Wonder Woman. It's precisely for this reason that no one bats an eye when the simple act of throwing a red/green crystal gives rise to a giant fortress in the middle of the Arctic. There's simply no need to explain the science behind it, as the "alien" backstory is presented in a way that's comparable to magic-based fantasy. Sure, we get a quick little explanation for the way Supes' powers work, but that's it really. Pretty much everything else that has a foundation in Kryptonian culture gets a free pass, and it's a free pass by association (i.e., because Supes is an alien). It's almost akin to being lulled into a willing suspension of disbelief. And in some small way, that conditions the mind to accept other questionable things, such as the aforementioned mild-mannered disguise.
But we're going around in circles now, and as it seems like you're still kind of struggling with the fantasy component in the mythos (which, to me, is so obvious and separate from any kind of "soft" science that ultimately fails to account for the character's many wondrous gifts), I don't know if it behooves us to continue this discussion much further. Secondly, if I recall correctly, you're a self-professed specialist in superhero science. And personally, I don't think there's much practical value in that subject beyond the viewing experience, where it mostly functions as a device to help audiences better engage with—and thus enjoy—a given fantasy concept.
In other words, were you to accept that there's a much larger fantasy element at work here, it could fundamentally change the way you approach your beloved pastime, that is, the so-called "science of superheroes." Hence, we'll always be at a standstill.