The great thing about Amazon owning the .mobi format is that it can merrily fail to document it properly and cause people to waste a lot of time scratching their heads.
Since the Kindlegen sample contains nested navpoint entries I think you can assume that those will work fine on the Kindle and that you don't need to convert ncx files made for epub. The class definitions in the ncx make no sense at all - 'class' is not an allowed attribute for navpoints and the selectors aren't defined in the sample's css. I would suggest not bothering about them.
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