"Just for my curiosity, I would love to understand how Adobe managed to get the specs of the iPhone byte-code."

It isn't bytecode, it is a binary on a commonly used platform (ARM).

But in general, somewhat a moot point seeing that Flash apps compiled using this method are already in the app store at present, as well as a variety of other applications made using things that aren't Apple's SDK. As long as you abide by their restrictions it doesn't look like apple cares what you program in.