Fix tracking of X11 window native geometry

If the xwayland scale factor changes and the logical geometry needs no re-adjustments, then the native geometry of the X window won't be updated. It will look as if the client window only occupies a small part of the window until the user resizes the window.

This MR switches relevant geometry bits to the device pixels so it's easier to track what geometry has been requested. However, in order to accomplish that (without introducing another layer of "last geometry" properties), this MR also reworks how the managed windows are configured.

closes #226 (closed)