Here is Novel's response. My guess is tools like MonoTouch are unaffected.
http://www.mono-project.com/newstouch/archive/2010/Apr-09.html
My guess is what Apple is trying to stop, are tools that do not use Apples APIs. So for example, a button needs to be a button from Apples UI tool set, and not a button from Flash's tool set.
I can understand that, and see why Apple wants to control that sort of thing.







