Adding an extra bug here. I notice that the Cosmic Store is not functioning by default in the Atomic version of Fedora 42 Cosmic. Nothing is shown as already installed, there are no software icons and attempting to install any available flatpak does not initiate.
If I enable Flathub (not enabled by default) this changes and this error is resolved.
RPM-Ostree upgrade via the terminal does appear to work though.
Update: Cosmic store default to testing flatpaks. Changing the pull-down to system Flatpaks allows installations to take place.