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No need to adjust if you do the NCX/TOC in advance, then point KindleGen at the linking .opf. Or even just the zipped-up ePub file (though obviously not if you wanted to autogenerate the TOC from NCX).
If you were adding after the fact to an extracted .mobi, yes. But until then, it's all just input from the original sources, which can remain as-is (besides a couple of minor specific things you have to do to the .opf make sure the .ncx and any .html TOC get picked up properly by KindleGen).
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