I just had a quick look at the gnome-software flatpak backend, and it doesn't seem to call flatpak_installation_list_remote_related_refs_sync(). This is the method call that looks at all the refs that are "related" to the app and wheter you should automatically install them (flatpak_related_ref_should_download) with the app.

In particular, this will return the Locale extension with the "proper" subpath subset that should be used (flatpak_related_ref_get_subpaths), and available extensions such as the OpenGL driver that pairs with a runtime. This later is required to automatically get the right nvidia drivers if needed when you install or update a runtime.