Usually, teams that square off in bowl games have at most one or two common opponents. Riding your analysis on one game when college football teams have such a variable level of performance is dangerous, and that's made obvious here. Ute fans will point to the Michigan game for evidence that the Utes are significantly better, and BYU fans will note that their margin of victory in the Utah State game was vast compared to how the Utes did.
In this case, margins of victory overall give a slight advantage to the Cougars. Overall, they went 126-93 while the Utes went 102-72.