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This idea is about how I imagine ideal automatic-window-placement system. I don't know how this mechanism works currently, so I asks how it works currently.

On X11 probably it's impossible. I think compositor cannot get information when window was redraw lately in X11. But on Wayland it's quite possible, because apps shares window buffer with compositor and must send signal 'window is redrawn'. We can store time of last redrawn operation. Also, we can store each mouse click position and remove it after some time.

What I would achieve? Window never popup/shown on position, which were updated lately or on position, where user click lately. There couldn't be case of misfortune click on popup or window will cover movie or game window. It also can replace do not disturb mode in some cases, when game window are on full screen for example. When we pause game window or movie window, popup could appear again. When we start movie again, popups couldn't appear above movie window.