Flatpak cannot access host's installations
The Flatpak of GNOME Builder cannot access the system-wide installations of the host flatpak. Since
/etc is mounted at
/var/run/host/etc the bundled flatpak doesn't find the configuration files.
sysconfdir at build time or the environment variable
FLATPAK_CONFIG_DIR=/var/run/host/etc/flatpak must be set to fix the issue (for most users).
Version: 3.34.1 from Flathub
System: Fedora 31