Apple doesn't want anyone to create iPhone apps outside of the Xcode/Objective-C environment. How can they actually enforce this?
If the non Xcode IDE, for example Unity, compiles to an iPhone executable, how will Apple know which dev environment you used to create the app? Can they have Xcode compile some sort of signature into the executable that no one knows about?
For tools such as unity, corona, flash, and other platforms used to 'generate' iphone apps, Apple may be able to 'decompile' and examine your app (look at patterns of generated functions, etc). From this, they might be able to guess that your app was generated with such a tool.
In the limit, this is impossible. Consider the following: I write some script code to generate a bunch of objective-c code. Then I manually import the objective-c files into xcode and build the app. How would apple be able to distinguish the script-generated code from human-written code? Maybe I just tend to write code that happens to look machine-generated. There's no way for apple to determine whether the code was "originally written in objective-c, c, c++ or javascript" or not, yet this would still, technically, violate the agreement. That's why the 3.3.1 part of the agreement is nonsense.
I believe that many of these translator tools have some kind of common runtime function library which take care of the portions that could not be translated 1:1. Those function could then be pretty constant regardless of your application. That way there would be no real need to decompile the app. but instead just look for usage of those function signatures.
FWIW I find the whole idea of limiting user's choice of tools is a bad move.
Most automated systems do things a particular way, which isn't hard to detect. If you've ever looked at the PHP or JavaScript code Adobe Dreamweaver generates, for example, you know how easy it is to find stuff like this.
Apple is doing this to prevent people from using Adobe's Flash development framework. It should also be noted that Apple's decision to limit Application Frameworks like this is causing the DOJ/FTC or some government agency to start an informal inquiry into monopolistic practices.
From this article: "According to the Post's Hollywood source, Apple's ban of Adobe's Flash technology on the iPhone and iPad is what prompted the government to poke around. "
They really don't have an issue up until now with other frameworks because Adobe didn't have one based with the Flash environment. Now that there is one, Apple is going to restrict anything that talks/looks/smells/acts like an Adobe Flash app on the iPhone. In my opinion, they won't do anything to other frameworks, but they'll enforce the rule just for Adobe. Which brings up the whole monopolistic practices thing.