Mark,
My wife made the same suggestion. A valid one and I'll propose it but as Lyman suspected, the alternate would impact one of the hooks of the race in that it boasts a net drop in elevation. While the net drop would remain the same, the elevation profile of the course would show a sharp incline for the alternate course.
This would be another reason for potential trouble if two finishers were disputing placement if they ran different courses. One is markedly more difficult than the other.