I usually use em for font-size and indent. I like that to scale at the same level. Margins are by default set by pt, I want small margins no matter the font size. I like to utilize the screen as much as possible. Sometimes a book calls for a larger margin, for example when a letter is in the book. I usually set those also to pt, I would like to differ the margins with the normal text, but not grow with font size. This would prevent that the screen would be too small for the text.
I almost never use percentages though. Perhaps with smallcaps or headers.
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