I wish people would look at things from a production perspective and get their history straight.
The original half color/half black and white version (which is in the TOS R S3 set) has that same audio change for the keeper line at the end. That was one of the shots they cut out for Menagerie. When they found the remaining color footage for the subsequent restoration, that was apparently all they found. The audio element was most likely lost or damaged beyond repair. Remember, we're talking about physical film and audio tape media here, not digital data.