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
In my experience updates aren’t that big. The flatpak cli ux is just confusing to read how much data actually has to be downloaded because of deduplication.
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.