I can't really believe this - if both parties agreed an alternate contract was made orally then the court would effectively rule against both parties in favour of supporting a knowingly false contract?
Yes, but that's not what was claimed. Of course if it can't be established that there was any further [alteration of the] contract then the written contract will be relied on. But that doesn't really seem to be the heart of what the Four Corners doctrine is about.
FWIW the Wikipedia definition, http://en.wikipedia.org/wiki/Four_corners_%28law%29, contrasts sharply with your use and doesn't really seem to speak at all to overwriting of terms by further contracts.