The Calibre naming convention is not amenable to change. The way is stores books is built into the guts of the programs and thus not easy to change.
It is a good idea to think of the Calibre set of files as its own internal database - and in earlier releases of Calibre it really was physically a database rather than a file structure but that grew rather large as book collections grew.
Kovid has said it may change in the future - but certainly not in the near future.
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