What about Web apps that are added to the home screen? Well, it turns out that those apps don't actually run inside Safari. Rather, they are executed inside yet another app, called Web. Obviously, this app has not been allowed to execute dynamic code, although the reason why this would be the case is not clear at this point.
Will Apple allow third-party apps to use Nitro?
Looking to the future, it's likely that Apple will solve this problem by using a technique known as split processing, in which the browser's rendering engine will be essentially kept into a completely separate execution space from the app that hosts it. This approach, which is part of the upcoming Webkit 2 engine that Apple is developing, ensures that the browser can be provided with the appropriate privileges without causing the latter to spill into the hosting application as well. When that happens, we should finally see Nitro and its speed-ups become available to all developers.
Of course, it's entirely possible that Apple is at work on a completely different solution. As you can see, however, there is a perfectly logical explanation why things are the way they are—one that, incidentally, doesn't need to ascribe any nefarious intention to the company. Regardless, I am sure that Apple's penchant for secrecy will manage to keep the conspiracy theory enthusiasts busy for years to come.