Earlier quoted context omitted.
Why do you think that "windows" are the appropriate level at which to consider things, rather than a hierarchy in which one first choose the appropriate "application" and then switches between windows for that application, if more than one exist? Using a "single UI" to do two different things seems like an odd choice, albeit clearly one you're used to.
Not the GP, but I routinely have use-cases where I switch back and forth between (say) two windows of one app and one window of another app. That, is, for a given task I have a “working set” consisting of windows of different apps, involving more than one same-app window for at least one of the apps. It would be annoying to have to switch between different keyboard shortcuts, instead of just getting LRU behavior with…
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.