Several of the things listed are false (like the lack of ability to open files with your keyboard, which you can do with cmd-⬇) and app window switching (cmd+~)
How can you configure macOS to have a keyboard shortcut that also makes sense on ISO keyboards to switch between all windows of all apps in a single UI?
My point was that people tend to favor whichever approach they're most used to. Switching only at the window level does "lose" information about the hierarchy, while switching with the hierarchy in place requires one to track the hierarchy which they might prefer not to do. One is not necessarily better than the other, and there are use-cases for both.
The problem is “for a given app”. If I want to switch back to the previous window, I have to use a different shortcut depending on whether that window was from the same app or not. Similarly, if I want to switch back to the window before that, I may have to first use one shortcut to switch back to the other app, and then use the other shortcut to switch within that app. If the windows represent documents, this roughly means that when switching between documents, you have to use a different shortcut depending on whether the type of the document you’re switching to happens to be the same or different from the one you’re currently on. This isn’t really intuitive, and arguably entails more cognitive overhead.
I agree that a lot comes down what you’re used to, but there are also good reasons to prefer one approach over the other.