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Allowing the user to set the parameters would be ideal. However, there isn't a universal way in which paragraphs are encoded.
That's why automatic converters like Calibre will sometimes fail to make the adjustments you want.
Sometimes the paragraphs themselves aren't within html tags but the inter-paragraph space is. There are other oddities like that.
In those cases, the only solution is to manually change the code yourself.
BTW, I set my regular paragraphs with a 4% indent and 1% top-margin.
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