Then here's what you'll have to do. You'll have to make one version for iBooks and one version for everything else. iBooks is an oddity unto itself and you do have to code differently there (not always, but a good portion of the time).
For example, font-variant: small-caps will not work with ADE based Readers/apps. So you either have to embed a font with a true small-cap font or fake it in the CSS like most publishers do.
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