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.
This would only work on single files or archives, but yes probably a good idea. I think cryptomator slices up files into equal pieces and then encrypts both, protecting against analysis of file types, but being sync-friendly.
Probably not an ideal solution, but you could script CLI bcrypt or openssl-ing the files tar-ed and then just rsync or whatever to a location. Organizing by original file hash values would provide unique identifiers that don't surface the file type without the observer knowing the OG filename and your salt
No, I don't have an answer to your question. But I have one: is there a reason you aren't using a backup tool with integrated encryption, like restic, for this? It sounds as if you're doing encrypted backups, but the hard way.