iBooks Author is a tool designed to enable authors of instructional, and other interactive content, to format their work specifically for distribution on iPad devices. In time these parameters may change but, for now, this is the purpose that iBooks Author serves.
If you are authoring your content directly in iBooks Author then I suggest to you that you’re doing it wrong. Create your work as you would have previously and then approach the idea of publishing it on the iBookstore as an opportunity to spruce up your presentation with interactive elements.
iBooks Author is a tool that allows you to leverage specific advantages of the iPad and iBooks 2. It is, categorically, not a tool for creating cross-platform “electronic books”. If you’d like to create those then Apple will be happy to provide a first-class experience for them. If you’d like to do something above and beyond that then consider iBooks Author.
Why the hell they opted for a restrictive EULA when they have such a terrific pitch is beyond me.