Flatpak: yes, it's about making that. But to make an app for a distribution where I don't know the environment, you need some kind of common denominator for the environment. So flatpack does some of that, and freedesktop does some more.
The needed outcome is for freedesktop to have an application distrubution story - which is effectively the same as if flatpak had a larged application interoperability idea. The fact that this is two separate efforts highlights the problem - you need everything to be a coherent whole.
A combination of a larger and more modern desktop api compliance effort PLUS an app distribution effort like for example flatpak, would be perfect.
E.g. "here is how you build an app for linux desktop v5". You include the right headers linux_desktop_sound.h, linux_desktop_dpi_notifications.h, linux_desktop_dpi_scaling_events.h (etc.). I know in the end an API on top just makes you have N+1 apis - but that's the reason this whole thing needs more dictator/ivory tower. It shouldnt' be be called "freedesktop-flatpack", or "somenewname" it should be called "linux desktop apps v1.0". This is probably the hardest part: getting the politics together. For desktop to succeed you need to have an ivory tower somewhere, in the middle of the bazaar.