I think you’re mixing up iBooks and iBooks author. iBooks the reader app is based on epub like Nook, Kobo, Sony, et. al. iBooks Author extends the ePub format to introduce interactive elements, but it is possible to publish a fully compliant ePub2/ePub3 from iBooks author. The real issue with iBooks Author is if you plan to sell the book you are only licensed to do so through the iBooks Store.