R1 vs R2 prioritizes graduate research output. Which is what the PAC12 values.
Most academic ratings focus on undergraduate education. Which is what BYU values.
Neither of those are "wrong", they're just different. Mercedes Benz makes busses for public transport, see them all over Germany. They also make the S-Class, which is a nicer luxury car.
That said, I don't want to use the S-Class for public transit and I don't want the Mercedes bus in my garage. They're both "better" than the other, depending on context.