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Good typesetting systems (like TeX) have some clever algorithms to find the best set of linebreaks possible, this takes into account the whole paragraph, and not just on a line-by-line basis, considers hyphenation and allows for character protrusion (optical margins) and font stretching (to an unnoticeable extent, but making a different in the visual spacing). There's no reason why an ePub reader could not use some slightly more advanced algorithm that the "typewriter" engine we usually see...
Anyway, a book should not specify any alignment, or font, or line-spacing, or margins... except where needed for particular designs. Those features should be left to the reading software to apply. Relying in a reader's ability for overriding is a bad idea. If I have a centered paragraph in a normal book, overriding would set this paragraph as justified, or left-aligned, or whatever.
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