The MOBI file is for Amazon; the ePUB file is for the other eRetailers. If you’re a print layout client, you’ll upload the PDF that we give you at KDP Print, Createspace, IngramSpark or whichever POD (Print on Demand) company you’re using.

Fixed-layout ePUBs made from InDesign will NOT magically turn into fixed-layout MOBI files at Amazon!

One thing that we run into, often, is the mistaken belief that an InDesign user can output a fixed-layout ePUB file, from the Adobe InDesign program, and that if you upload that at the KDP, magically, a fixed-layout MOBI file will emerge.

IT WILL NOT.

If your InDesigner tells you it will—it won't.  If some idiot who has self-appointed him/herself as an 'expert" on some forum—anonymously—tells you that it will—it won't.  I don't care if Jeff Bezos himself tells you that this will work—it won't.

Why Not?

It won't work because, quite simply, the fixed-layout specifications at Amazon are completely different than the Apple-centric fixed-layout specifications that are output by InDesign into ePUB format.  Quite simply, it is the proverbial apples and oranges.   The specifications that make fixed-layout work, on a Kindle, are significantly different than how fixed-layout ePUB works, on an Apple iOS device.

So, don't waste your time, or your money, trying to make a fixed-layout ePUB build a MOBI/Kindle file at Amazon.  Quite simply, it doesn't work.