Perhaps the epub has the margin already set inside it? Try opening the epub using the "Tweak epub" option (shortcut: T) and look at the .css file to see if there are any large margins set. I find that a lot of epub books like to have 1em or even 2em margins, which depending on your font size could be around 2cm. Since I read on an iPhone and such large margins leave me with only 3-4 words per line on the small screen, I'm very sensitive to this and end up editing a lot of epubs to de-marginize them.
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