shell-app-system: Give priority to .desktop IDs that should be shown

If we have multiple desktop ID's that share the same startup-wm class
and none of them is actually matching the desktop-id, then we should
exclude the ones that should not be shown in the current desktop.

This will help preventing cases such as the previous one in case no
desktop file ID would match the startup-wm-class exactly.

Part-of: <https://gitlab.gnome.org/GNOME/gnome-shell/-/merge_requests/2721>