Fedora already has two “warnings” when it comes to their own packages.

First, Gnome Software shows a verified badge for all Flatpaks that are maintained by upstream. The Fedora Flatpak does not have this badge.

Second, when installing a Fedora Flatpak, the label “Fedora Flatpak” shows right under the install button

Sure, this isn’t perfect. Non-technical users may not understand what these mean. But it’s not like Fedora is intentionally trying to mislead users.