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
I have like 4 gigs of flatpak updates I keep unchecking because at my horrible internet speed it would take the entire day if not more to download. Honestly, if you’re right then this is a horrendous design flaw.