I can't really say if BYU has had a good or bad strength and conditioning program. I'm not in any type of position to make a judgement on that. But I do know that the S&T coach at any school is responsible for hundreds of athletes. In reality, the S&T coaches can only spend a very short period of time with each athlete and make in impact in their regimen.
Meanwhile, players graduate, seek at a dedicated S&T coach for the upcoming draft and are suddenly surprise by the effect of a dedicated coach that is getting paid big bucks to give you personal attention. You can't compare the two situations at all. Plus the extra time you are putting into S&T and suddenly great improvements occur.