Since going independent, BYU has won 39% of their games against P5/ND opponents.

Utah has been maybe slightly better than median P5, but pretty close to median. So you'd expect Utah to win more often than not, but not absurdly so.

If BYU has a true 40% chance against Utah each time, you'd expect 3, maybe 4 wins in a 9 year span. Odds of losing 9 straight would be ~1%.

So either there's been a 1 in 100 type of bad luck or there's something which makes BYU particularly poorly suited to Utah and means BYUs chances of winning are much lower than would be expected given the relative quality of the teams.

That's the scary part. If it's just bad luck, then that sucks for BYU but doesn't predict anything. If it's something that makes Utah particularly bad for BYU (whether that's scheme or QB attitude or expectations or whatever), you'd presume that will continue.