So, yeah, flatpak is horribly inneficient on disk usage and can easily take 60GB if you are a bit generous on app installs. 60GB is, notably, less than 1.4TB

Out of curiosity, how did you search for what was using up the space? Did you try apps like baobab or filelight? One of them is usually preinstalled and they have not failed me yet (except when hard-linking or copy-on-write is involved, but that shouldn’t show up on the global disk usage percentage)