As I understood it, the two APIs have different purposes, so I don't think you can really compare them.

Origin Private File System is for files that the app manages internally and that normally, the user should never touch - like stuff in /var or AppData for native applications. Hence why browsers make no guarantees where on disk they will store those files or even if they'll store them as files at all.

But I think that's not really very interesting, because it's not offering anything new you couldn't already do with localStorage or indexedDB, just with a file-like API. Hence why browsers also put it in the same "ephemeral local data" bucket as those APIs.

The directory picker API would offer a new ability, namely to "open a directory" in user-managed space and work with it like an IDE would. But I can see why the security risks are too large for that.