That said, if you have a secure trusted machine with FDE that you don't let strangers touch, and where every piece of software is well-isolated (for example, web browser is sandboxed and can't access the ~/.password-store/), then yeah, filesystem permissions will do the trick.

But, for example, if you sync using git repo hosted on some third-party VPS then directory permissions won't protect you from that host owner or whoever gains superuser access to the filesystem.

(Hey, don't downvote the parent, he didn't said anything wrong, just asked a question! In my opinion that contributes to the discussion.)