Based on Sage's training, one could tell he wasn't going to qualify. He kept cutting his workouts short, always saying "saving it for the race." Once you shift into that mentality, you are done. You are over-thinking. You need to stress the body past the point of comfort in training.
My 2nd thought (although Smyth ran 63:00 today) is that MUT racing slows the stride by generating too much power and vertical velocity. His stride has gotten slower but stronger and to get his propulsion forward, he needed more time on the flats at fast paces. At least now he can focus on what he is great - MUT racing and throw down some epic races.