Quote: "Apple provides the Xcode toolkit for free and makes no restriction on the distribution of OS X applications created using it, but one can't help thinking that it's only a matter of time until that happens."
Impossible. For one, the major components of Xcode are open source - Xcode is simply a front-end for the tools.
Secondly, and more importantly, a vast amount of development done with Xcode isn't relevant to the App store (mobile or otherwise), e.g. device drivers, plugins, tools, etc, etc. Apple has made it abundantly clear that iOS and Mac OS are designed for different purposes, and even the Mac OS has different audiences in mind, i.e. professional vs consumer. Quite simply, Apple won't have anything to deliver to consumers if it loses the professionals. Anyone who thinks Apple doesn't know that is frankly naive. Put another way, can you imagine that Apple's plan is to entrust development for all Mac/iPhone content to MS Windows? Not a chance.
IMO the restriction on the output from the iBooks Author software reflects the immaturity of the whole eBook market, e.g. weak (but developing) format standards, wildly differing hardware, and generally rubbish distribution. Apple is trying to carve out an entire, coherent ecosystem for the creation, sales, and consumption of eBooks that 'just works', and so the parts are necessarily bound together. Outside of the iPad, there isn't much of an alternative for viewing these documents anyway (not consistently at least). The publishing industry, like the music industry, has tried to avoid the digital revolution rather than embracing it. And in doing so, they leave a huge, gaping opportunity for a company like Apple to define how it works.