I'd have to disagree with you on the build once, run everywhere philosophy. If you're talking about mobile apps, there's really no such thing. And textbooks (at least as Apple sees them) are a subset of mobile apps.
It takes specialized environment to make a device specific application and now text book. However, I have read that Apple is keen on ePub 3 standard so perhaps we'll see an export function to make an ePub 3 formatted book in the future. Right now, the iBook Author tool seems to have only PDF as the export function.
It also exports an ".ibooks" file, which is an epub file with a different filename extension. This is the file that gets shipped to ibooks.
It looks like standard epub, with some additional files (so it _should_ degrade.)
Apple put some ncx extensions (looks like thumbnails) into a separate file, and referenced it from a meta tag in the .ncx file. They added their usual com.apple.ibooks.display-options.xml file, that they have for their fixed-layout epubs, but I think they're using CSS for layout in the new files.
The xhtml/css generated from their app doesn't render well in a browser or calibre. I suspect that's because of their use of avant-garde css features (e.g. @page ). I think these files would be able to degrade to other epub readers with some css tweaks.
"You may distribute books created in iBooks Author free of charge on your own website. If you wish to sell your book, you must do so through the iBookstore."
http://support.apple.com/kb/HT5071#3
Does that mean you can't charge money for your output unless it's through the iBookstore? In other words, you couldn't publish for-purchase work to other eBook stores like Kindle?
It takes specialized environment to make a device specific application and now text book. However, I have read that Apple is keen on ePub 3 standard so perhaps we'll see an export function to make an ePub 3 formatted book in the future. Right now, the iBook Author tool seems to have only PDF as the export function.