I agree this should be exported by the flatpak package. I haven't hit any other packages putting anything in /etc/profile.d, though that does happen I know (so perhaps Guix should incorporate or patch such things?). Flatpak is also due for an update soon I think, so that would be a good time to make the modification perhaps.
bug#44997: Flatpaks are invisible to application launchers
John Kehayias via Bug reports for GNU Guix Mon, 16 Aug 2021 20:02:15 -0700