As I noted elsewhere, I wonder what kind of patent protection if offers to downstream users of derived products. Since BSD-ish licenses don't mandate the passing of redistribution rights, I must assume the patent protection (like OpenJDK users enjoy - much to Oracle's non-enjoyment) isn't there.
I am not saying Apple wants to patent-troll downstream developers, but that's a risk that's worth noting.
It's a peculiar exception - and Apple is almost certainly never going to be in violation of it. Still, the point is that Apple's lawyers are terrified that it could somehow taint iOS/OS X/iTunes if someone comes to believe that Apple might be in violation of it. Why take the chance? Clang is a compliant and fast c/c++ compiler at this point, and is mostly clean code (which is more than can be said of gcc).