A standardized structure is possible when you are thinking about a relatively homogenous colelction on a single operating system and a single file system. calibre is designed to work across multiple OSes and multiple file systems each with different restrictions on valid filename characters, file name lengths, character encoding and case sensitivity rules. In such a scenario, using a filesystem to store metadata, which is what you are advocating is simply not a good idea.
Note that calibre can export its database in both XML and CSV formats, for interop with other software.
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