Are you sure? It looks like you found the main problem already.
I’ve been struggling with this issue for years…
You’ve already detected one of the biggest problems – compatibility. I wrote a book about Stencyl, and it didn’t do very well. It was basically an iPad only book, because it was built in iBooks Author – before ePub. While I like how it turned out, it didn’t matter. Stencyl runs on Mac, Windows and Linux. So, a large percentage of the target audience couldn’t read the book.
While the iBooks Author widgets (that Hype can create via project exporting) are great for creating interactivity, the support is limited – even as an ePub. I don’t know of anyone but Apple that supports it.
Another alternative, if you want to use Hype, is to create the project as an app – and then publish it under the book category in the iTunes App Store. This is a lot more work, but the iTunes App Store is probably more popular than the iBooks Store. (Although, the competition is greater on the iTunes App Store. I could hit #1 in a category on the iBooks Store, not so easy in the iTunes App Store.)
I don’t think this is a common thing. When you try to convert a traditionally print document to the web, it usually doesn’t translate well. So, either design a website or design a book. What’s the point of trying to make a book as a website?