The goal of any cross country team is to be ready for the big race at the end of the season. Allegheny was ready when it counted the most.
Most likely it is not an "upset" but rather they came under radar.
Why did they come under everyone's radar?
First, because they focused on the end of the year, not on the earlier parts of the year in which polls are based upon. And, second, because national polls are not a true measurement by any means, especially for cross country. There are so many things that the polls do not and can't measure when conferences, regionals, and nationals come along.
The hype around national polls should be flushed down the toilet. I don't know who does those polls, but consider this: The polls going into nationals were highly incorrect when comparing to the actual finishes at nationals. For example, the polls had 4 midwest teams ranked in the top 10 (2-5-8-9). At nationals, the midwest went 9-11-13-25-26.
Getting back to Allegheny, I believe that in general, the entire mideast region came under the radar, likely due to the polls. Entering nationals, mideast teams ranked were 6-14-23-33 (Haverford, Allegheny, Carnegie Mellon, and Muhlenberg). At nationals, the mideast went 3-10-12-29 (Allegheny, Haver, CMU, and Muhl).
I should point out that Claremont-Mudd-Scripps entered nationals ranked #28, and finished #16. Likely they're the only team that the "mudd" helped. Harvey would be proud.
Congrats to Allegheny. You earned your third place finish.