the app devs dont care about flatpak rules and store secrets outside the app container, meaning the app is unconfined by default, you need to manually add an override and it is still pretty insecure in the case that all untrusted apps are flatpaks
KDE KVaults only supports insecure algorithms, goCryptFS would be the most secure for local only stuff, but that was abandoned as a Fedora package and is only available from COPR, currently. (I should learn RPM packaging once again).
Cryptomator seems to be the only one 1. Suitable for cloud sync (not encrypting everything always again) 2. That passed an audit.
The CLI may be fine if it just interacts with the GUI app? I wonder how that would work with the Flatpak.