1) Heaps wasn't sub par material. He didn't get specific stength and conditioning training for his position. Seems Omer's process includes a "what good for the goose is good for the gander" approach.
2) Reynolds wasn't sub par material and projected high in the draft before his workouts after the season. How many blue chip linemen do you have to have - who don't make the NFL - before you think there may be a problem?
3) The team, especially early in the season, simply ran out of gas in the second half of each of the first 3-4 games. Take the Utah game or the Texas game as fine examples.
4) BYU has, in most every year, had a higher ranked recruiting class than Utah. This has been the case, with few exceptions for decades. Utah puts more guys in the league and it isn't just technique but also strength and conditioning. So, Utah, with lesser thought of athletes than BYU, based on recruiting boards over many, many years, has basically twice as many players on active NFL rosters than BYU does, since 2001 - when Omer started. Boise the same. TCU the same.
There is evidence that this may be an issue. Although there are other factors than just S&C and Omer that you can point a finger at too.