Desktop file broken in flatpak
The flathub build fails to start from the desktop file, because the .desktop file has:
python org.gnome.Keysign -m keysign
as the Exec line, and it has to be "python3" in the runtime.
However, flatpak run works, because the command specified for that is just "gnome-keysign". You should probably change the desktop file to do this too.