Does your ebook contain a com.apple.ibooks.display-options.xml file? A few years back, I seem to remember needing that when generating epub2 books. My notes mutter about needing to add "<meta property="ibooks:specified-fonts">true</meta>" for epub3 files.
Hope this is of some help.
Edit: Check the
Apple Books Asset Guide 5.2.11 for the metadata for epub3 font embedding.