The origin file system is pretty pointless, but it is only one part of the spec. It is definitely intended that the local file system (whether a cloud k/v store or not) at least allows for moving data between completely different websites.

I think you make a good point about Safari's nonsense with browser data. The spec should require implementors to never clear out what they use for "local file system" unless the user explicitly says to, and only for the files selected for deletion. The old APIs like local storage/IndexedDB unfortunately assumed no browser vendor would be as dumb as Safari with their ridiculously short retention policy.