It has only a little to do with altitude. It has more to do with intelligent racing. CU didn't gun for it, they let the race come to them in both races. They started off controlled and finished strong. The conditions were terrible and the course was going to run very slow, and CU adapted the best.
Stanford's women flew out of the gate and paid for it over the last 2k. Luckily for them they have so much talent that they could implode and still beat the field.
On the men's side, the individuals that won were not the ones pushing the pace or worrying about moving 3k-4k in or surging here or there. The ones that did faded. The ones that didn't and sat patiently in the lead pack, finished 1-2-3. CU's men were not winning at 5k, but it was almost clear they would win even before the race began. They did it in 2004 under the same conditions because Colorado races intelligently, and that's the best way to race in muddy, sloppy and SLOW conditions.
I don't think they were a "huge underdog." The women might have been, although they proved at Regionals that they can race, but not the men. Only those who don't understand XC (wejo, rojo?) think they were huge underdogs. They were first at pre-nats, presumably the second best (maybe third, slimly) team in the land the whole year behind Wisco. And if I knew the course would be muddy and slow, I would have moved CU up to first in the polls, because they've proved before and will prove again that Wetmore knows how to train his runners to run intelligently, especially in those conditions.
And yes, there may be a bit of "altitude builds aerobic fitness" stuff that may in fact HELP teams and individuals like CU in slower, more difficult races, certainly Baumgartner of SUU may not have been third in an all-out fast race (the difference between strength running and speed running), but altitude did not equal success uniformly at nationals this year. It was smart running, ultimately, and that's what CU accels at.