The lock-in would be complete if they change iBooks to only display books that have been published with their variant of epub classes. They don't do this, so would have to agree that you can produce your book any way you want then make it available.
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.