Wouldn't hidden files require a different extension? That would make the files unusable unless converted back to the original by calibre. Presently, even though the files are stored (organized doesn't really fit here) is a folder/filename structure unique to calibre, the files are still identifiable and usable outside of calibre should calibre become unusable in a future OS (unlikely) or the user decides to use something else. By being able to specify where calibre's folder goes, a user can ensure the file will be recognized by most, if not all, automated or semiautomated back up schemes.
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