Ah, good point. That feels win-win then; package maintainers get a huge efficiency win by just synchronizing on their base packages but they're not locked to them so they can make things work without littering up the user's global library space with oddball versions of dependencies.
https://blogs.gnome.org/alexl/2017/10/02/on-application-size...
I can't speak for the others, but Flatpak is a layered solution, so files are deduped and shared across the layers (runtimes, applications) that need them.