I am a life-long die-hard Cougar fan. But I am also a realist.
It's easier to have a higher winning percentage when you play an easier schedule (e.g., WAC or MWC versus PAC 12 or SEC). If BYU played a full P5 schedule every year, it would most likely have fewer wins. That's what happened to Utah for the first few years after they moved from the MWC to the Pac 12.
It would be interesting to compare BYU's winning percentage against the top 20 winning teams versus the other top 20 winning teams' winning percentages against each other. For example, BYU's winning percentage versus the other top 20 winning teams versus USC's or Alabama's winning percentages versus the other top 20 teams. I suspect BYU's winning percentage versus the other top 20 winning teams would be significantly lower than most of the others, most of whom play other top 20 winning teams much more frequently than BYU does.