That's basically the case. The Amazon format is basically a proprietary wrapper around epub. You make a Kindle file by starting with an ePub file and running it through the Kindlegen software provided by Amazon. So Calibre's converters are basically reverse-engineering that process. This means that if an ePub version of the book is being sold by Apple or Kobo or some other vendor, that's the file you should start with, though their encryption may be better than Amazon's.