The problem is InDesign is built around the concept of a fixed-size page layout and hard-coded font sizes, but it has others sizes built into certain structures (e.g., tables).
If one were to layout a document on a page which approximated the size of a typical ebook reader, the results are much more readable. Not perfect, but at readable and workable.
Best thing is to encode the entire document in a sensible form of XML which can capture all nuances of the text such as TEI and then convert to dump into both ID and epub.
William
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