From the feature list APFS supports per-file encryption. Hence by extension it should be possible to setup an encrypted folder (or at least just the files within that folder) with a password that is different than the user login password. Similarly, it should be possible to encrypt users' home directories with their own respective keys, and render them inaccessible to one another despite whatever their file permission says (similar to what Windows' NTFS able to do since the previous century).
The question is that how to do that from a user's point of view? I've yet to see any UI in the Finder that can do this in macOS High Sierra. Is there a way in the command-line to enable this?