Apple's strategy for their phone platform runs deeper then just what is in the open source Webkit codebase.
I used to think/hope open platforms would ultimately win in the market but iOS and the Apple App Store has kind of proved otherwise.
If people want to run web apps on iOS devices Apples is more than happy to sell them for that purpose.
The most closed thing I can think of is when they only enabled their faster JS engine for the browser itself and not for apps. The next major release changed that, and it is not related to WebKit itself.
Apple is actively (Frequent commits) working on fixing this problem. The project is called Webkit2, and features a Javascript interpreter that runs in a separate process, and thus is able to safely execute Javascript on iOS. This model, btw., is inspired by the multi-process architecture found in other major browsers.
For one, i ditched the kindle app ever since i discovered read.amazon.com .