I spoke to a couple of folk who are familiar with the e-publishing biz, and apparently most of this is (sadly) par for the course! Even when using the tools Amazon and co supply for ebook authoring (read: converter), you end up with shafted deals like these. There's not much 'authoring' to these tools, and as such is closer to a wav->mp3 sort of things, or how iTunes is only for apple products.. and where Palm was not allowed to sync with it. (If this is common knowledge; I apologize... I was under the impression at first that this was a MS Word-like program, and that whatever you typed in there would be subject to these terms... but thankfully it's not _THAT_ bad just yet.)
There's only a few small differences. For one, this converter Apple makes available can do some extra stuff, and is better at a .epub conversion than many other programs, especially for the less tech savvy ebook author(wannabe)s. People don't care about the extra ibook-only stuff, but they are upset they can't get to use it for the epub converting stuff. Finally, there's the matter how you don't get to see the EULA till well into the program.. while you already agree to it the moment you start the application, which is pretty sleazy as well.
In the end, it is Apple being horribly greedy Apple, trying to lock people in on their platform once again like how they did for the iPuddle and IPhiddle. They basically supply a free tool that woos everyone (especially the fanboys drinking the koolaid), get people to using it, lock them in, and do everything to restrict the user... like many other big companies out there.