It is indeed a take to assert with a straight face that official adventure design is both desirable, good, and the baseline that the game should revolve around.
Seems to me that you have an irrational hatred for flying PCs and have no qualms engaging in cognitive dissonance to assert that hatred.
You may clutch thine pearls at being accused of all that but I simply cannot believe you can be as interested in DND as you are and simultaneously believe that official adventure design is even remotely good when its universally panned, and deservedly so. Either you're carrying an extreme minority opinion (doubtful) or, as said, you're jumping through hoops to attack something you don't like for whatever reason.
And as it happens, you instead missed (re: ignored) the point, which was that worrying about having perfect counters to all PC abilities in every single encounter is a waste of time, particularly given that doesn't really make for satisfying adventures anyway.
You want a healthy mix of encounters that challenge and don't challenge, and any mix inbetween. Variety matters, as does the need for players to actually feel that they aren't on a pointless treadmill. Those set piece battles are where you want to put that effort in, because those are going to be the ones that you aren't going to be resolving in half a round.
But even then, theres nothing saying that goblin duo can't be played in a way that can still challenge a flier; thats why the battle map itself is important. A flier with a longbow doesn't have that big of an advantage in a tiny cave that happens to have a cieling within the goblins shortbow range, but even then, different environmental objects can be used to even the odds, and the choices both sides have to make to try and tip the odds in their favor are what you actually want anyway.
A longbow flier that has to make considerations of where they place themselves in a tiny, crevice filled cave is better than them automatically winning because you put the battle in a blank white room.
Something I like to point out is that even lowly bandits can put up a threat against level 20 characters with the right battlemap, and if played with intelligence you can even make such an encounter just as consequential as 6 ancient whites in a blank room.
When you approach encounter design this way, you don't have to throw out PC abilities like flying, because it fundamentally isn't a given that those abilities negate all of the encounters difficulties.