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You are encountering the difficulties of converting textbooks, scientific books or any other book which requires exact fixed formatting to epub. Epub is not only not designed for fixed formatting, but is based on flowing formatting which changes to match the text size.
PDF meets this goal, but it does not scale well to smaller devices as it becomes unreadable. But this would be true of any format.
It is possible to reformat the book so long sections of formulas etc are broken up. The shortcoming is that support for special characters is somewhat spotty. You can replace them with images. But all of this means you are spending more time formatting than studying.
Regrettably, this sort of material might be better read in pdf on a small notebook or a larger tablet whose screens are closer to the size of a sheet of paper.
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