I still believe that the parameters for how an ePub "looks" should be tied to the device it's being read on (and effectively giving the control of the look to the individuals).
There are too many different types of eBook Readers to have a "one size fit all" line of parameters, and the output is usually very different from publisher to publisher.
I'll say it again : tie the parameters (margins, justification, etc) to the eBook Readers, NOT the ePub file itself. Plain and simple. Shouldn't be too complicated...