The overall records of the teams is irrelavent. If Utah had been left in the WAC, they would likely not be where they are today. BYU forced MWC to bring Utah with them. Had BYU left Utah behind, Utah would probably have fallen further behind BYU. A similar situation happened when Utah had the chance to join the PAC 12, but Utah didn't insist BYU come along (not that they had the influence necessary to insist anything), and now the gap between the teams is spreading. It is logical to conclude that without BYU, Utah would have fallen farther behind after 1996.

Also, you could argue that BYU's lead in the series began in 1965 and lasted til 2001. It's all about how you gerrymander the numbers. Such arguments are unconvincing to anyone that doesn't already agree with you.