I would not consider the default applications on the iphone "apps" even. They are written by Apple to provide a certain functionality and that is what they do. They can use any API they need. Why should they not use private API? I would not consider iBooks to be somehow different from say the phone or system preferences "app". They are there because they are provided by the system.
Bundling IE was never the problem. Using private APIs to give IE a noticeable advantage over other, more popular browsers in an effort to gain marketshare for IE was the problem. Having a monopoly isn't illegal, and is part of capitalism. Using a monopoly in one market (say, operating systems) gain share in another (like, browsers) is.
To me the issue with IE and Windows was that MS went from a position where IE basically didn't exist (but other browsers did and worked fine on it's OS) to "it couldn't possibly not be tightly integrated into Windows" in no time at all.
Funny how Microsoft owned 90%+ of installs globally. Just because everyone copies apple doesn't mean everyone uses apple and needs to bend to their will. It's the opposite actually.
That should only go as far as the app store and the settings app. The rest of the applications on the system have no reason to be special for they don't need special system administration tasks to function.
Android even functions where nothing is a 'special' app. (Although no phone is actually released that way, but it can be achieved with custom ROMs).
