The footnote and backlink as DiapDealer shows them will work just fine in a Kindle ebook.
I am pleased to see KDP issues discussed here. Given that Amazon, for me, sells 80 percent of digital editions, I compose first for the Kindle platform and only secondarily in epub. I upload html to the KDP, ignoring Kindlegen, Mobipocket Creator, NCX files, and all that stuff. I then open the html in Sigil and tweak it a bit for Barnes & Noble.
Yes, I will someday go back and figure out how to add an NCX file to my ebooks, but at the present time I am too busy and too happy with the results to slow down my production of new and backlist books.
Someday I may even acquire a Mac and publish to the Apple iBookstore, but that is at present the least of my concerns.
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