Disagree. The fact that these are independent is a huge organizational boon for those who know how to apply some combination of them.
Example: I set up spaces (virtual desktops) to have themes: one of general web, one for iOS dev, one for Android dev, etc. within that, it’s useful to be able to further organize with windows and tabs — windows can represent projects for example, and tabs can represent files. These work together to prevent a Cambrian explosion of windows that would be impossible to manage no matter how your environment works.
It’s useful for apps to be distinct from windows, too. This allows things like moving all windows belonging to a particular app between screens, or minimizing/maximizing them all, hiding them all, etc. Panes in most circumstances are an entirely different beast than tabs and windows… it wouldn’t be useful to turn an inspector palette into a tab.
They work together as long as one’s mental model isn’t overly simplistic.