Jabari would have still been a #5 pick if he had come to BYU---maybe still #2.
Is the coaching better at Duke than at BYU? Probably (I like Rose a lot, but Coach K is a legend), but I don't think it really plays out much in terms of NBA drafting as so much of the draft is based on potential.
And BYU's system has definitely elevated some people to get drafted higher than otherwise they would have (Jimmer/Araujo)