Application Z requires another 3GB because it needs Gnome runtime version X+1, not version X. Although I do believe Flatpak does some kind of reduplication so actual used space is somewhat less.
It's also less of a problem if you flatpak all the apps vs having just a handful. The more apps the better chance they're actually sharing runtimes.
Flatpak updates are handled very smoothly by KDE Discover, I always assumed Gnome Software did the same, so no additional package manager required.
Despite the few downsides Flatpak is still wonderful. As a Kubuntu user it's nice to say Farewell random PPAs whenever there's a need for an actual newish version of an application
Teslas have internal driver monitoring cameras? :O