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calibre flattens all CSS. That is the only way that automatic processing like font size rationalization and fake margin removal can work. It also greatly lowers the load on viewers reading calibre produced epubs. That is one of the reasons that doing an epub to epub conversion in calibre will often make a non working epub work. calibre is *not* an ebook authoring tool. If you care about the exact contents of your final epub, create it by hand.
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