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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
That's why I think AppImage is the best. Despite needing to pack everything it needs it's always far more lightweight than flatpak. I'd rather download a 50mb appimage than several gigabytes of an entire OS libraries and then the updates requiring roughly the same size. That and I have a shitty internet
I fell for the lie of flatpak not being bloated, I just nuked flatpak from my PC since I just run arch anyways. Im not sure if repo is safe to remove. You might be able to run rmlint -g and see how much data can be deduplicated on an FS level, I never checked myself since I run f2fs, but if you run an FS with dedupe capabilities it may work for you.