Thank you Lynx for bringing davidfor's solution out from being buried in all that technical CSS thread, I completely missed this answer to that very annoying problem. It's easy to see how Kobo missed this bug, since before 2.3.1 the margin on sideloaded books was zero regardless of what setting you used. Hopefully they'll fix it in the next firmware.
And big thanks to davidfor again. That's the second time in a week I'm in you debt, after also helping me be finally able to display Hebrew books the right way.