It turns out there is a known issue that reports the gio-launch-desktop problem (see https://issues.guix.gnu.org/issue/38135). The problem is fixed, but the fix is not in production yet. However, I can confirm that the workaround described in that issue report fixes all the problems I mentioned in my original messages.
So, opening files through Thunar on Xfce, Caja on MATE and Nautilus on sway works correctly if you modify your system configuration so that it imports "(gnu packages glib)" and adds "(list glib "bin")" to the list of packages.
