I'm not sure as to the entirety of what is supported on the ipad and not however I can tell you that margins are supported. I export my epubs from indesign and indesign automatically applies any spacing in the paragraph style as margin or text-indent. The ipad honors those values in turn.
What the ipad does NOT support is the page-break property, widows and orphans and more. Nor of course does it support embedded fonts. You have 6 on the ipad to select from, and in the case of non-roman languages, it appears to be only 1 font. Hope that helps, All the best/c