If you want to read epub using books (formerly ibooks) containing embeded fonts you will need to include the file com.apple.ibooks.display-options.xml in the META-INF folder within the epub.
This file contains:
<?xml version="1.0" encoding="UTF-8"?>
<display_options>
<platform name="*">
<option name="specified-fonts">true</option>
</platform>
</display_options>
This will update the iTunesMetadata.plist file when transferring.
This file can do much more depending on what settings you decide to put in it. The above is just to allow embedded fonts to show. There is more info on search engines.
Hope it helps.