I believe the original author's pain is around the paucity of good EPUB publishing tools, and to have one appear with these restrictions makes them sad. It would have been nice if Apple had said, "If you buy a commercial license to this software for $X we won't constrain your ability to sell the books produced." Then at least there would be a way to use to the tool to produce books that would be salable at both Apple and Amazon's shops.
Clearly Apple sees this as a way to build a library of 'exclusive' content in iBooks and mute the Kindle threat. For me at least that shows me just how threatening the Kindle Fire is to their model.
Hell, iBooks Author exports PDFs. PDFs are viewable by Kindle Fires. (And possibly other Kindles.) So iBooks Author already creates content viewable on competitors' platforms.
I'm also not certain the Fire is threatening to Apple. They make far more money off of the hardware than they do off content sold through their various digital media stores.
iBooks Author is not a reaction to the Kindle Fire. Apple has been working on this since before there were rumors that Amazon was going to introduce a tablet of their own.
Steve Jobs even told his biographer about it . Jobs passed away in October, a week after Amazon announced the Kindle Fire.