I do think that looking into the developer terms is a fantastic thing. I think developers should use whatever they're best at to create the program, and then change it into all the separate platforms.
Even to the detriment of a platform, and even if it doesn't translate that well. This sort of thing is only to evident when you see some of the "well written for Xbox360" graphical engines ported to the PS3. The code just doesn't translate as well, because the PS3 can't play all of it's fancy tricks due to the Xbox 360 having no branch prediction logic and the PS3 being able to better handle resource and task allocation itself. Those game engines (not looking at GTA IV..much) suck ass on anything but the original platform.
But...I'm not a programmer. So is there a specific reason not to allow the use of these third party apps besides simply maintaining the heavily controlled environment of the iFamily?
Yes, the third party layers which abstract the iPhone SDK APIs are actually hiding them from the developers (except for MonoTouch). Instead the APIs are hidden by a simpler, dumbed down, one-size-fits-all interface provided by Flash (in this case).
Also, I feel like I'm one of the very few who still likes Flash.
You are a dying breed, that's for sure