What exactly is the wish?
Read-only files in a custom folder tree? Would it be enough to generate a fake directory tree, on command, using something similar to what save templates does, but with symlinks, like BetterRed described?
One obvious problem is the current optimization with lazy update of metadata in the ebooks, metadata is only written to books when the books leave calibre or when manually launched. To change that would slow down calibre a lot. So to generate the fake tree you would first have to write metadata to books, then create all the symlinks.
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