Switching to epub3 only for page numbers might not be such a good idea for Amazon KDP authors, because, AFAIK, KindleGen only supports NCX pageLists or ADE page-map xml files.
Also, last I checked, Amazon KDP didn't support "real page numbers." AFAIK, only big publishing houses who offer both print and Kindle books can offer Kindle books with "real page numbers" on Amazon.
Moreover, KindleGen apparently only supports the ePub3 items listed in the
KindleGen 2.8 release notes, and nav page-list isn't listed.