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This is just the way that pdf conversion works. Original line indents and other text formatting aren't preserved. (aside from bold/italics, which are)
This works ok for novels, but as you noted isn't the best for many textbooks. There may be some commercial tools which may be able to do a better job at pdf to html conversion (not sure but have seen other users mention they exist). If you can find something that does that Calibre can convert the html to a epub from there.
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