Nearly 20 years ago there was an OS X screensaver that would capture all the window buffers and then float them around the screen as they rotated various ways. Another app would save a snapshot of all windows as Photoshop layers with appropriate transparency (before blur was added). X11 was always network transparent, though I don’t think windows could easily be moved from one client to another.

Even classic Mac OS, which wasn’t designed to be “rootless” could be run that way could have its windows mixed with OS X windows in the classic days.

As others have pointed out, there is already a PoC app that is doing it, so it seems if Apple wants to, it’s completely in their power. However, does this match their vision? (pun intended) Time will tell.