Maybe create a separate partition and encrypt it so it asks for a password on mount, then unmount it when not in use?
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You can store files in a keepassXC database.
Cross platform you're sol, I'm afraid. If there's an option I'd like to know, too.
Usually I cover my requirements with acl in this case.
I understood op is talking about devices like an external hard drive, in which case any Linux only solution (based on fuse) won't work for windows and similarly the easy nfs encryption option on folders wont work with Linux.
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It can work on an application layer
You can use 7zip to archive files into a .7z and protect it with a password. 7zip is cross-platform, it's available for Windows, Mac and Linux.
Edit: sorry, I see you have already evaluated this option. I don't know another method that would me more transparent.
That is massively insecure
Password protected zips are very easy to brute force so I wouldn't use them for anything