Also spent about 20 minutes trying to figure out how to use the #GZDoom flatpak with mods. Then I remembered that #Lutris has its own zdoom runner. Worked on the first try.
@thrickles What distro are you using? Most of them has gzdoom in their repo. There are couple of other source ports as well, but worth checking the version. Also, good job, finding a solution! :)