The Xcode example is already a reality. If you produce an iOS app using Xcode, you have two choices: sell it for a price in the App Store and pay Apple a cut, or give it away.
I would not be at all surprised if the Xcode EULA contained language enforcing this now that you are no longer required to have an ADC account (free or otherwise) to download Xcode.
The greater point stands. If Apple had made iBooks Author only able to publish to the iBookstore, no one would have been surprised. It's their platform, and they do as they please. Don't like it, don't use it. I know a few publishers that are making this very judgement call right now: build our own web-based platform, or pay Apple's vig. Sure, they'd love to use Apple's tool for free. They'd also like to stop paying $1200 for Adobe's Creative Suite, but that's not happening either.
* The Xcode example isn't a reality. I can see my Mac application outside of the appstore without giving Apple a penny. I can sell my corporate iPhone / iPad application without giving Apple a penny (corporates can obtain management tools that allow them to load applications without using the appstore). It's true for a subset - consumer iOS apps.
* I've had Xcode prior to it's free availability in the appstore and have never had an ADC account - it was on the CDs with my MacBook.
On the first point, I was specifically referring to iOS apps, and you cannot "sell my corporate iPhone/iPad application" in the way you describe. Side-loading is only available to businesses with more than 500 employees, and as far as I understand, is only for internally developed applications.
Fair enough on the second, but it's tangential to the point. Apple constrains the distribution channels of iOS apps built using Xcode. This specific case is analogous to the iBooks Author tool restrictions.