xdg-shell: use toplevel geometry to adjust the popup box

`popup_unconstrain` uses view coordinates to init the output box for
popups. However wlroots expects the box to be set in a toplevel surface
coordinate system, which is not always equal to view. The difference
between those is a window geometry set via xdg-shell.

GTK4 reserves some space for client-side decoration and thus has a
window with top left corner not matching to (0, 0) of a surface. The box
calculated without taking that into account was slightly shifted
compared to the actual output and allowed to position part of the popup
off screen.

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