Flatpak Support
Flatpak has become a popular format and Gnome Software officially supports it. With the proxy change mentioned before, flatpaks work, but some nuances exist depending on the template.
Fedora Templates
In Fedora templates, flatpaks come with an fedoraproject.org “remote”, which makes it already possible to search for and install flatpaks.
Debian Templates
Debian, by contrast, provides no default remote. In practice this means that users need to install add a “remote” to be able to install Flatpak.