Rockd - I don't know what they would do. I've read other posts where this has been mentioned as well so I'm pretty sure it is correct. In fact, I had a small rock chip on one of my 19" OEMs and Rickrack - a superb detailer - couldn't make it perfect although he fixed it to the point where only I notice it.
The standard silver BMW wheels are not an issue as they are painted. The warranty probably was written to cover those wheels. However, since they issued it to you, I would think you have a good case to argue that they would need to fix them.
This is in part why I am going with the silver finish on the RAC buy - the silver finish can be fixed but not the anthracite or gunmetal finishes.