For a "championship" is almost as flawed.
More importantly, but not included in your "timing" argument, is that BYU timed their undefeated year for a year there were no others...
All major polls (not just AP) picked BYU as #1 after they spent 3 weeks as #1 and finished the season undefeated and #1.
Utah never reached #1 mostly because there were other undefeated and obviously better teams in those years. That is the real timing/issue causing the difference.