Insofar as "rational fiction" is rational, it's just good fiction[0].

If we tack on the requirements that it "teach rationality" and "deconstruct" some setting, then maybe you might justify it as a separate genre, but in all of the works that I've read (and I've read the entirety of HPMOR, as well as a few others on that list), they seem to miss why characters might behave in an apparently irrational fashion.

See, there's a convention in fiction where sometimes the author can't describe the precise evolution of their fictional universe in a step-by-step manner, and so they just skip to the next incident in the plot, or maybe paper over how some feat was accomplished with a weak explanation.
As long as it doesn't interfere with the point of the story, it's just something you, as the reader, are supposed to accept.
For example, to provide a scientifically plausible explanation of the biomechanics of Prometheus' regenerating liver[1] would detract from the thrust of the myth, and might also have been difficult to do given the state of medical knowledge in Ancient Greece.

Deconstructing things is fine (and usually shows up to some degree in all fanfics, not just self-consciously rational ones).
It's a fun intellectual game to wonder just how exploitable various magic systems are, but perhaps the story that Rowling wanted to tell hinged less on precisely how magic worked than on the timeless tale of plucky schoolchildren successfully killing their teacher in a secret dungeon.
Ah, youth.

But the problem with HPMOR and related works is that, when you start trying to enforce optimal decision making at every single point in the story, you tend to end up ruining the story either through reducing it to absurdity (c.f. the conclusion of the book, which involves multiple simultaneous decapitations using transfigured nanowire), or doing so much worldbuilding that the plot starts to collapse under its own weight.

HPMOR barely hangs together thanks to the efforts of Rowling, who managed to paint a sufficiently vivid universe that Yudkowsky could write ~137,000 words in order to tweak the magic system and also do a pastiche of the mock battles in Ender's Game.

And as far as teaching rationality goes, I'm skeptical.
It wasn't that Harry was transcendentally rational, just that almost every other character was exceedingly dull.
The places where he demonstrates his supposedly amazing thought process tended to be when blackmailing people who could easily retaliate, a couple of basic experiments, or jargon-dense recapitulations of obvious ideas[2].

Not to mention that the dubious rationality of a plan for creating safe AI whose first step involves writing a fanfiction for a children's fantasy series.
I've seen Yudkowsky justify it in various ways, but it seems to me that he just likes to write and tried to make his personal project more relevant to his broader goals.

I know, I know, that's probably excessively snarky.
But still, it is exceedingly frustrating to see people advocating for more "rational" fiction without understanding how fiction works.
I haven't read everything listed on the site, but for my own part, "rational" fiction is far from a silver bullet; in most cases it's just a necessary (but not sufficient) criteria that good fiction has to fulfill.

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0. "Actions should be logical and follow naturally from actions that precede them." via, https://en.wikipedia.org/wiki/Poetics_(Aristotle)

1. https://en.wikipedia.org/wiki/Prometheus#Hesiod_and_the_Theo...

2. ... about half of which were wrong or incomplete. Charitably, you might say this reflects Harry's precocious but not-fully-developed mind, or if you were less positively inclined you might say that teaching people incorrect things is the opposite of promoting rationality