I just picked the first and latest WotC settings. If it's a stark comparison, it's certainly not by contrivance. You've got Dark Sun, Eberron, and Forgotten Realms. I could probably write a "desert adventure" that would fit any of them, but I would have to provide alternative encounters for all three. Dark Sun stuff is very different, as best as I can recall, FR and Eberron don't have the same kinds of critters and cultures in the desert regions as each other. If I want to do a "city of the elves"... that's not going to happen. Too different. In theory, I could write an adventure that could for Thay or the Dragon Kings, in the general, but all the stuff is going to have to be modular.
If I write a Generic Medievalish, it's probably not going to work with any of the published settings. So who do I sell it to? 4e fans who don't play in any of the published settings? In practice, I have to pick one of the settings and write for it, with adaptation to other settings being of secondary concern.
Again, you're cherry-picking ideas that are difficult to fit between the settings. And a 'generic medievilish' adventure would certainly work for either of those settings, and possibly dark sun, also.
You can draw an arbitary line to support your argument, but that doesn't mean anything. I can think of dozens of scenarios that would fit well in either Eberron or FR or Krynn, Greyhawk, ect, ect. A substantial subset of DMs have their own world, but adapt scenarios and other details to it based on existing source material. How do you think these people operate?
In practice, as a developer or DM, you certainly don't have to pick one of the published settings, and that's quite abundantly clear from how people use them and build them, and the years in which generic scenarios and dungeons have been on offer. You are arguing that it is not feasable to do something which people, both publishers and DMs, have been doing successfully for decades.
This is also all, WOTC's stated approach to modules in most cases. It's also their stated approach to their world design! A third party producer does not face any distinct issues which make it harder for them to create scenarios that can be adapted to various settings. There may be related issues like deity names, ect, but frankly those issues are trivial compared to the essence of good scenario design.
And that brings me back to this: I can't use their fluff, but I have a limited ability to write my own without making my product uncompatible. And FR doesn't need a generic Waterdeep, since it already has the real thing.
This is once again simply false. There's nothing stopping you or rather, a DM, from adding your city to their Faerun, or Eberron, or Toril, or Krynn, or whatever. And they are likely to be able to do so with minimal conversion. Almost all settings have room for this kind of thing, and FR and Eberron make a point of it.
And writing fluff, even detailed fluff does not render a product incompatible except in a minority of cases. If I write a detailed history of an ancient temple to the sun god which is now in ruins, guess what? It could fit in any of those settings. If I invent a knightly order, complete with laws and chapter houses, ect, no matter what you may argue, the average DM can and will slot that order into their Silver Marches or their Solamnia just fine.