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