That's the best you've got? An airy statement that says that "Magic can alter anything - bear that in mind when worldbuilding"? Well yes. That's obvious.
If it's obvious than it seems that you, at least, concede the point. Very good, we will move on unless ProfessorCirno posts a rejoinder.
But there is a world of difference between saying "This exists." and saying "Here is how you deal with the following problems." As far as worldbuilding is concerned, the DMG paragraph above takes the problems into account in the same way that making the button bright red and slapping a "Do not push" sign over a base self-destruct button takes into account the chance of someone trying to blow up a lair.
If you want to take issue with the advice given, feel free to write a review of the DMG. The point under contention was whether 3e ever, at any point, even once, purported to simulate a realistic world. Since it stated that it assumes a realistic world, I hope you are ready to concede that point, as well.
But the point you are failing to rebut is that the sort of magic present in 3e completely unbalances the world. The magic is strong enough that any attempt to build a "fairly realistic world" is like building a castle on quicksand.
Nonsense. D&D can be "fairly realistic" or nonsensical, just as with comic book RPGs, or Cold War espionate RPGs, or any other genre. You can use the DMG guidelines, as written, and simply by keeping most communities after 50,000 people (as they were during most of the medieval period) you will see the amount of magic and magic items shrink to very manageable levels. Sprinkle the world with metropolises, and you have the Forgotten Realms. But a "fairly realistic" setting is not a function of how magical it is. Eberron is a very magical setting, yet many people enjoy the sense of magic belonging in the setting. I'm not a huge Eberron fan. I was raised on Mystara and Greyhawk, so "medieval drag" appeals to me. In 27 years of playing D&D, I have yet to find the assortment of spells and magical items an impediment to the existence of a believable world.
And as for the "ban certain spells" approach, that's simply the Oberoni Fallacy.
No, it's not. The rules look exactly like the world of a standard D&D game. If you want the world to look differently, you will have to modify and prune some elements. But as it stands, D&D's assumed world has been the basis of many successful, internally consistent campaigns for decades. Specifically, I ran a level 1-20 campaign and not once did I feel the campaign world was unsupportable simply because it was fantastical. I have never banned a single core spell, class, or feat from my games.
3e can not even support its own worlds with the magic flying around unless you either go all out gonzo with a comic book world (Forgotten Realms) or relatively low powered and start from the principle mages will attempt to break any normal economy (Eberron).
In other words, it can't support it's own worlds except that it can and does. Simply disliking the Eberron approach or the FR approach does not mean those approaches are not a valid approach to world-building. Living Greyhawk took a third way which you glossed away; mid power levels, with gonzo elements less common and more isolated in the game world. Greyhawkian D&D with its feudalism and relatively medieval-esque militaries and economies has also been a viable approach, again, for countless campaigns over the past few decades.
4e on the other hand keeps strategic resources (i.e. the resources needed to unbalance a world) in check far more and thus is much more flexible for worldbuilding.
Unless you want to put those resources into the hands of the PCs, in which case you are worse off than you started. Actually, in my view, the ability to endlessly produce a magical effect is a much larger obstacle to world-building, because it makes it impossible to build any world in which magic is rare and mysterious. If I were going to adapt 4e to my preferred style of game worlds, I would have to replace the wizard's zot powers with... I don't know, crossbow powers or something.