Doesn’t distrobox (and podman) come with SteamOS these days too?
You wouldn’t be able to layer, but using distrobox-export from inside a distrobox container would let you export command line apps as well as graphical ones too. The graphical apps will even show up in your menu and can be pinned as well.
(Of course, if something is available on Flathub already as a Flatpak, installing the app via Discover is easier and better. While Flathub has a lot of apps, it doesn’t have everything, so being able to pick and choose from any distribution using distrobox is nice for a very large selection of software.)