If you charge a fee for any book or other work you generate using this software (a “Work”), you may only sell or distribute such Work through Apple (e.g., through the iBookstore) and such distribution will be subject to a separate agreement with Apple.
Here's the new language:
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.
See, the problem with this is that the new language still covers other formats. If you take an iBooks file, and then disassemble it (so you can edit it), when you put it back together the resulting Epub will be "a work that includes files in the .ibooks format generated using iBooks Author".
An Epub made from parts of an iBooks file by definition contains files made with iBA, so that Epub is controlled by Apple just as much as the source iBooks file was. The only change today was that Apple wanted to make it clear how thoroughly they control the ebooks you make. If you were hoping that Apple might loosen their control, well, you don't know Apple.
P.S. If you disagree with my interpretation, please note that I am using a pessimistic interpretation. This is what I think one of Apple's lawyers will decide the EULA means should it ever go to court. It is probably wrong on a technical level, but the argument could still be made that my interpretation is valid.