The idea is that it’d allow for smoother updating rather than having to run between updating flatpaks and then using the CLI of choice. It’d also make it easier for new users regarding gnome.
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Software supports updating distro packages via packagekit. Does that doesn’t work for you?
Mine is namned package updater. Seems to be for all packages, no matter if flatpak, i think? But maybe it could be named something different, like how the gnome program “camera” does camera things.