I understand all of that. And that is precisely my point. Isolate everything concerning an app to its own window, and allow that to be maximized. If an app has multiple windows, contain them within the main app window. Don't pollute the "global" window space with app-specific windows.
> If an app has multiple windows, contain them within the main app window.
This advice is actually rarely followed by apps regardless of whether they are on Windows or Mac. Consider Microsoft Word; if you open two Word documents, does Microsoft Word open two windows or does it open one main app window and then contain both documents in a single window? Are you aware of this Microsoft concept called MDI?
It sounds like you were used to iOS where each app has but one window and you'd prefer that to be the case on desktop operating systems like Mac or Windows. There's nothing with preferring that, but it's against decades of desktop computing tradition.
That makes it really hard to use two (or more) applications side-by-side effectively. I am grateful for individual windows I can move exactly to where I need them without worrying about the application as a whole. I think it boils down to how people think — application-centered thinking makes it easy to have multiple windows from different applications playing nicely with each other, workspace-centered thinking hates what appears to be the messiness of applications having windows here and there.