Disclaimer
Flatpak uses OSTree, like Fedora Atomic Desktops (Silverblue, Kinoite etc) and similar to BTRFS snapshots.
So many files are deduplicated and linked, not actually there
https://gitlab.com/TheEvilSkeleton/flatpak-dedup-checker
50GB without
31GB with deduplication
21,4GB with BTRFS compression
Yes but that is unimportant. This is not user friendly at all. I do that all the time for random stuff, but especially on GNOME the system hides stuff like that away from users and thats okay.