It could just be that they're built with slightly different, durable muscle. When Prefontaine lost to Viren in Munich, he simply did not have the muscle durability to continue a hard pace, but Viren did despite having less muscle than Pre. I don't see how the "aerobic" argument can be used here because Pre had one of the highest runner Vo2maxes ever recorded (84).
I think these skinny but fast runners have more potential than anyone else, but it's occasionally wasted by high mileage training. Only bigger guys should try more mileage to get leaner and lose unnecessary weight (IMO). But skinny guys don't have that problem. Skinny guys should pick up weights to recruit more of their genetically durable muscle.
This way, they can run at an even higher speed (because of the muscle, look at 100-400m runners), and be able to maintain that longer than normal guys due to their gift.