If i use Distrobox to give me the dnf package manager and use dnf to install software (like sudo dnf install godot) and then use the distrobox export app command to make it available from the Discover menu, would that work?
Yes, distrobox-export --app should work on Fedora atomic too, given that the command basically creates a desktop file within the host user’s home folder.
If instead of Distrobox you’d use Toolbx, given that it is preinstalled on Fedora atomic desktops, then you’ll need to create the desktop file manually.