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They queried that info based on a specific implementation of a framework. If that framework is implemented under Wayland, then through the Wayland APIs it will only get rudimentary info on mouse position (e.g. only when it’s in focus and the mouse is over it).

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App doesn't have to be in focus. It receives pointer events over its own surfaces (plus in some additional cases like drags and grabs). It doesn't receive any information about pointer position otherwise, nor its global coordinates (at least not without extra protocols).

Is it possible that one could write essentially a transparent app, which is always in focus and just passes click events through the transparent layer?

You can write a transparent app, but its the compositor that decides whether it's in focus and your app will either pass both hovers and clicks to the window behind (not staying in focus for long and not getting any pointer events even when it still is), or it will consume them all.

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