While Apple’s explanation is certainly plausible, it does seem they are trying very hard to place blame anywhere other than on themselves. After all, if previous generation iPhones had no such issues, why would the 3GS be any different? The company has made many design changes with the 3GS, and though this situation may’ve not been predictable, Apple cannot say they played no part in it.
They did offer one suggestion for fixing the problem: cleaning the back of the device with rubbing alcohol. This seems to validate that the device itself is in no danger of becoming discolored from heat, with the real source of the problem coming from the outside world.