I have often made this argument in the context of sandboxing communications software like browsers and e-mail clients, where it is relatively unusual to need access to local files except for their own data. In that context, restricting access to other parts of the filesystem unless explicitly approved would be a useful defence against security vulnerabilities being exploited by data from remote sources. It’s hard to encrypt someone’s data and hold it for ransom or to upload sensitive documents if your malware-infected process gets killed the moment it starts poking around where it has no business being.
More generally, I see no reason that we shouldn’t limit applications’ access to any system by default, following the basic security principle of least privilege. We have useful access control lists based on concepts of ownership by users and groups and reserving different parts of the filesystem for different people. Why can’t we also have something analogous where different files or other system resources are only accessible to applications that have been approved for that access?