You haven't overlooked anything. That's the way it's supposed to be. EPUB is supposed to be a pliable format, allowing the reader to reformat the text in any way the reader pleases. As opposed to PDF, EPUB is a reader-centric format -- that's why I love it, and that's why I avoid PDF files, which are publisher-centric. If you expect e-reader software to give you 100% of the publisher's formatting, you're bound to get disappointed, regardless of which e-reader app you choose. I love Moon+ Reader precisely for the opposite of what you're looking for: the plentiful layout customisation options on the user's side.
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