I haven't done enough with epub 3, so I am not sure about the nav.html. For kepubs from epub 2, the reader will use the ToC from the toc.ncx. But, it creates a ToC entry for any files in the spine that are not in the toc.ncx. My quick look at your epub 3 kepubs, it seemed to do the same thing.
Also, can you add a straight epub 3 sample? It feels like it is missing especially as the changelog under the list of samples has it as the second point. I expect it will be the same as the kepub samples, but, it would be good for non-Kobo or Kindle users. It might be a good idea to complete the set and add an epub 2 as well.
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