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
One gotcha is installing both as user and root, getting two sets of dependencies. I only found out after a year or so of consciously using flatpak.
I’m now taking care to make sure I only use flatpak as root. Maybe not the most secure.