Most issues should be reported upstream where they're more likely to be noticed. Flatpak-specific issues may be reported here or upstream.
The dedicated server included in this flatpak may be started with flatpak run --command=xonotic-dedicated org.xonotic.Xonotic. It requires additional configuration to be usable.
Config files, player/server ID keys, custom maps and other data are saved in ~/.var/app/org.xonotic.Xonotic/.xonotic/ (flatpak-specific).