Checking "Fonts" only removes font families from the css. Not much harm done with that. Ditto with color.
"Margins" and "padding" will remove all specified margins and paddings from the css, not only text margins, but also including those under the chapter headings, above and below sections, excerpts, letters, diary entries and so on. I don't recommend checking those. It would be like throwing the child out with the bathwater - too much formatting would be removed. The best way to remove annoying margins and/or padding is via editing the css.
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