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
No, that is about file system, not Flatpaks. Sure Flatpaks also use shared dependencies, but btrfs pushes it even further. I also avoided Flatpaks until switched to atomic distro, where flatpaks are primary way of installing apps. Common distros do not need them really, until you run some old Debian lol and you want newer software.
Ah, I was confused because you used a flatpak deduplication command. Okay, got it. So BTRFS with flatpak is what will do my head in 🙂