Do not create fixed-layout eBooks. They do not work in most cases.
If you are not creating a fixed layout eBook, take the ePub from InDesign and load it into either the calibre editor or Sigil and edit it. Make the code as simple as possible and make it well formatted with no overall L/R margins.
I've edited plenty of eBooks that have come from InDesign and it's not all that difficult.
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