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I have no idea, I dont use InDesign. I have seen InDesign produced EPUBs that are fixed layout and have tons of CSS which therefore take a much longer time to convert, so since I have not seen your EPUB, I am guessing it is one of those.
As for why kindlegen performs better, it's because it does much less than calibre. calibre produces MOBI files that look good from a far alrger colelction of input documents than kindlegen.
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