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Metadata is not stored in the filesystem, it is used in the filesystem and stored in the database.
The only solid requirements Kovid had when designing, I am sure, is giving calibre absolute dictatorial control over the storage, allowing every book record to have a unique location (hence ids), and the kindness of leaving it easily accessible via the file browser.
None of that is going to change. Your free-for-all suggestion will not be used anyway, although theoretically another rigid structure could be used, to no one's satisfaction.
On the other hand this was quite the original objection, it quite made my day.
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