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
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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.