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It's the downside of using HTML / CSS for eBooks.
Authors/Publishers go crazy with the styles [for unfathomable reasons - unlike webpages, ebooks actually look better the less CSS they have], some books don't even let you change the font. The preferred paragraph style (same for: justification, font, size, margins, ...) should be a setting on the reader and apply to all books... but that's not how it works.
In an ideal world Calibre would be superfluous but we don't have that, you just have to convert / remove offending styles / use external helpers for collection management / etc. the list goes on...
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