For what it's worth, I agree that longer tempo runs for shorter distances do seem counterintuitive. That said, my junior year in college my coach challenged me over the winter by having me do ventilitory threshold runs (really 30K-marathon pace), starting at 20 min and working up to over an hour. That, a fartlek/hills workout, and some easy mileage was really it for the time away from school. My second race back from winter break, and the first one that was really competitive, I ran 8:32 in the 3K, setting a 24 second PR in the process and going through the first 1600 (4:28) in the same time as my old high school PR.
I can't say for sure if it was the VT-long tempo runs, a continuing maturation process (I had run high 25s in the XC that previous season), or if I just had the race of my life at the time. But I really believed strongly in those VT runs, and still find them very efficient means of increasing stamina.