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Of course they can. It's built into the underlying *nix OS that both iOS and macOS are built on. This kind of nannying is soooooooo freaking annoying. And it is one of the many reasons why iPad remains a kid's toy, no matter how "pro" they make it.

They really can't. You can save files elsewhere, but that's the extent of it. Giving the appearance that an app's own sandboxed Document's folder exists in the same location as some shared unified user's Documents folder would be a nightmare for syncing, sharing and Continuity on iPhone and Mac.
 
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