Satire / parody doesn't necessarily have to be a merciless polemic against the target - and as a matter of fact, it would be pretty hard to read HPMOR and not come away with the feeling that the author was a pretty big Harry Potter fan.
Another thing that comes to mind is the horror movie Cabin in the Woods, which sends up lots of horror tropes but is still fun and enjoyable for fans of the genre.
[0]: Though carrying 4 combat application tourniquets in your clothing at all times is probably a good idea. The part about time pressure and disregarding time-wasting social activities in emergency situations is also reasonable[1], but the characters should have come up with contingency plans and gone over checklists and emergency conditions with the authority figures beforehand to prevent them getting in the way.
[1]: i.e. if you got stabbed and are bleeding out, don't tell someone "it's fine" (it's not fine at all) and let them go first because it's "polite".
The first few chapters of HPMoR are fine, I suppose. It's pretty lighthearted. But it rapidly devolves into unhinged ranting at extreme length. The last five hundred thousand pages are a vehicle for the "wisdom" of one of the most insufferable, unjustifiably arrogant, and misinformed people to ever draw breath.
Just go read Elon Musk's Twitter feed. Same experience, whole lot shorter.
https://danluu.com/su3su2u1/hpmor
tl;dr the science is bad, the writing is bad, the pedagogy/didactics is atrocious.
(interesting tangent https://shatterzone.substack.com/p/rationalist-harry-potter-... )
It's not "easy to miss". The author beats you 'bout the head with his ideology. It's heavy-handed even for something explicitly didactic.