Here's how the turn of events unfolded. Apple releases iBooks Author with loosely drafted EULA. Blogosphere overreacts. Apple says 'Hmm, looks like some people really overreacted to the intention of the EULA, we will have legal clarify the EULA.'
Apple has clarified the "important note" which mentions the intended use of the software:
If you want to charge a fee for a work that includes files in the .ibooks format generated using iBooks Author, you may only sell or distribute such work through Apple, and such distribution will be subject to a separate agreement with Apple. This restriction does not apply to the content of such works when distributed in a form that does not include files in the .ibooks format.
Many people claimed that any content you created in iBooks Author remained trapped as well. Apple has also clarified that this is not the case:
[I]f the work is provided for a fee (including as part of any subscription-based product or service) and includes files in the .ibooks format generated using iBooks Author, the work may only be distributed through Apple, and such distribution will be subject to a separate written agreement with Apple (or an Apple affiliate or subsidiary); provided, however, that this restriction will not apply to the content of the work when distributed in a form that does not include files in the .ibooks format generated using iBooks Author. You retain all your rights in the content of your works, and you may distribute such content by any means when it does not include files in the .ibooks format generated by iBooks Author.
It is good that Apple has addressed these concerns promptly in what I felt was a "non-issue at the time":http://julianyap.com/2012/01/21/why-the-emotional-criticism-of-ibooks-author-is-wrong.html.