wayland/shell: Apply geometry after subsurface state application

The subsurface state may affect the geometry end result, e.g. when
window decoration enlarging the toplevel window are applied. If we don't
wait with calculating the window geometry, intersecting the set region
with the subsurface tree extents will not include the subsurfaces.

Closes: https://gitlab.gnome.org/GNOME/mutter/-/issues/928

https://gitlab.gnome.org/GNOME/mutter/-/merge_requests/1295

(cherry picked from commit d6af5961)