There's ALOT more that goes into evaluating accuracy than just looking at stats. What type of offense is run and what type of throws is the QB being required to make. For instance, does he have an inflated completion percentage because he's throwing a large number of short passes, such as bubble screens?
Wyoming ran a pro-style offense under Craig Bohl, so Allen wasn't throwing a bunch of bubble screens. He was making more NFL type throws in college than other QB's coming out of RPO-type offenses. The average fan doesn't care about that and will just look at stats, comparing them side by side, when in actuality what the QB's are being asked to do is very different.