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Just so that you don't think everyone is ignoring your question...
I'm not aware of the internal workings (source code) to intelligently comment on the issue you've raised. I have a complex database, and lots of books, but I don't really make use of all of calibre's available "muscle". Pushing buttons and tweaking settings is one thing, altering the internal functionality a whole other issue.
I think that many of the other helpers in these forums are, for similar reasons, uncomfortable responding on the subject.
Thus, the question can only be answered by those who program calibre - Kovid Goyal, et al.
As for a better place... perhaps the bug report website (you'll need to register over there). I would see what Kovid says here first. Sometimes he'll do it from here, sometimes he wants a bug report to be submitted.
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