In the same way that "D&D is not D&D without Elves, Drow and Orcs" line is kinda bad?
Well, yes, actually. Exactly in that sense, though the closer analogy would be someone saying "D&D is not D&D if it has Dragonborn in it". This is a backhanded insult of 4E we're talking about here.
And, yeah, I'd have a complaint if someone walked up to a game I was running that didn't include elves, drow, and orcs (especially drow!) and said it wasn't D&D if I didn't include them in the campaign setting. The should be in the books as options because they have fans, but it would still be D&D if they get kicked out.
It doesn't do away with "[you can] change the cosmology to match what you want!" or even you can change the races to match what you want. D&D needs a baseline, for many years the great wheel was that baseline. For many D&D isn't D&D without it. They build the great wheel and anyone or everyone can discount it and make their own thing, just like what they can do with elves, drow and orcs. That doesn't mean they shouldn't make elves, drow and orcs. It has nothing to do about putting down 4e or saying the 4e planes are bad, it is about realizing and addressing that not everyone was on board with the 4e design.
I think you're being a little too charitable to the author's intent, here. Or, at the very least, you are missing a very clear reading of the lines that is anything but "not putting down 4e or saying that the 4e planes are bad". Whether or not that was the exact intent of those lines is unclear, but you need to put a lot of words in the author's mouth to get "this is about realizing and addressing that not everyone was on board with the 4e design" out of that particular line in the article.
First, I'm glad you liked the elemental chaos and astral sea, I can understand you even liking it over the well defined great wheel (and inner planes). That doesn't mean that they can't keep it or a version of it. I took aspects of the 4e cosmology for my game and integrated them with a VERY 3e cosmology base. It works great.
Second, I would want to see them evolve and advance the core cosmology instead of abandoning it again in favour of something completely new. They tried tearing down the cosmology and rebuilding it with similar (almost identical) pieces in 4e and that didn't work for many. I would have rathered something completely new but it seems unlikely as they probably want to keep nine hells and infinite (or 666) abyss layers. So, again, evolve and advance not rewrite from scratch.
The issue here is that I saw 4E as an advancement and evolution of the older Great Wheel cosmology. It wasn't a replacement, since it still integrated pretty much every bad idea that the older cosmologies had other than the strict ordering of planes, and pretty much every single location from the Great Wheel is easily placed into it (and is detailed in the Manual of the Planes). The 4E cosmology basically is the Great Wheel in every way except the physical (metaphysical?) structure.
If even a minor iterative change to the system (and yes, I'd say that 3E -> 4E is exactly that) is considered to be excessive or "rewriting from scratch", then the system is doomed to stagnate.
Third, I do like the idea of incorporating cosmology into the world. I think it works GREAT for a lot of mythical (real world myths) stories. Mount olympus is supposed to be in greece (iirc) afterall. A lot of what we would consider planar hopping is basically just them going to obscure or remote areas of the world. I think that a lot of these aspects DO NOT work in a lot of newer stories and certainly don't work well in games where you ARE going to be leaving your little plane behind.
I'm a big fan of the incorporating cosmology into the world approach myself. It is much more fun for gods and demons to inhabit the world itself, rather than be isolated off in weird alternate realms of existence that can only be accessed by certain high-level spells. If nothing else, I prefer planes that overlay over the physical world (like the Feywild or Shadowfell) over infinitely-sized theme worlds like most Outer Planes tend to be.
Fourth, D&D has always had a history of mixing up their cosmologies as it is. Eberron and Faerun both had different cosmologies than the default greyhawk one, and different again from spelljammer. So I don't see why that is so hard. I think the flaw for any discussion about cosmologies comes up when you try to talk about them in a vacuum without knowing the core world that they relate to. For example, I've never had any use for the inner elemental planes but I know countless games which have used them to great effect. Hell a notable NPC in my game has a cubic gate which links directly to the elemental plane of water, but it has never really come up.
Certainly, each setting really should have its own cosmology. I think it was a big mistake of older versions of the game to even establish a singular cosmology. The Realms, Eberron, Dark Sun, and others really need
their own cosmology, if they even need a cosmology at all.
I'm not sure if you strictly
need a world to reference to talk about a cosmology, though... Certainly, you shouldn't create them separately and then force them together, but if you create them separately and then interact with them separately, it still kinda works. The Great Wheel is terrible
as a core cosmology that is equally applied to every setting, but as a setting in its own right it isn't bad. The goal really should be to make the Great Wheel suitable for level 1 play, rather than make it the endgame for every other setting, if that makes sense.
Take everything I've said with a grain of salt, I just wanted to give my thoughts on the subject.
That's no different what I do.