Just read the new FAQ item, makes sense, but wondering about one thing. I realize Calibre always detects the existing metadata TOC, but it doesn't necessarily detect an existing human readable TOC that the mobi format uses, does it? I'm guessing (but not certain) that it might detect an existing human readable TOC if it already has an OPF/Mobi equivalent reference like this:
<reference type="toc" title="Table of Contents" href="filename.html#bookmark"/>
Reading further at this thread:
Seems to indicate that a human readable TOC could potentially be placed anywhere if OPF references it correctly.
My guess is the problem would be for the files which have a human readable TOC at the beginning of the document that's not properly referenced in the manifest. I don't think Calibre can detect this - I'm not arguing it should, any attempt to do so would definitely be a guess, as there would be no way to distinguish an index from a TOC for example.