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calibre has to support MOBI files that were created over a decade ago before Amazon even knew the word ebook existed, and before the MOBI format (which was not developed by amazon) even had the concept of an ncx toc.
For new MOBI files (i.e. KF8 files), calibre does indeed use the NCX toc. For older MOBI6 files, calibre will continue to use the content toc.
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