From what I know their TOS applies to everything which is posted to the Appstore. As hundreds of people already pointed out by the wording of the TOS, both Unity3d and Flash are in violation of it. It doesn't matter if Unity is a pre-processor or cross-compiler or whatever, the apps are not _originally_ written in objective-c, c++ or c.

This is the official response regarding their contact with apple:

"We haven’t heard anything from Apple about this affecting us, and we believe that with hundreds of titles (or probably over a thousand by now), including a significant proportion of the best selling ones, we’re adding so much value to the iPhone ecosystem that Apple can’t possibly want to shut that down.

Our current best guess is that we’ll be fine. But it would obviously be irresponsible to guarantee that. What I can guarantee is that we’ll continue to do everything in our power to make this work, and that we will be here to inform you when we know more – as soon as we know more."

source: http://blogs.unity3d.com/2010/04/10/unity-and-the-iphone-os-...