For what it may be worth, when I look at the ePub with 7Zip, I see the com.apple.ibooks.display-options.xml file in the META-INF directory. The contents of that file are:
Code:
<?xml version='1.0' encoding='utf-8'?>
<display_options>
<platform name="*">
<option name="specified-fonts">true</option>
</platform>
</display_options>
I think this is correct location and structure for allowing iBooks/Books to display embedded fonts.
One possibility for testing is to remove that file since the scrambled epub does not have any embedded fonts and see if the ePub then displays correctly.