Gregory's Server
Flatpak actually addressed most of the storage problems already. It has a diff engine that saves a lot of space if different apps use same libraries (even different versions can be deduped with only version differences being left out). That and compression makes flatpak apps take even less space sometimes then native packages if you already have the runtime installed by other apps.
@thor @bufalo1973
It's true that if you only have one or two flatpak apps it takes a lot more space but even if you install a kde app on gnome desktop with native packages it would take the same amount of space since you don't have the kde runtime so it's not comparable