Auburn was heavily lopsided toward the run, last year, so I can't see that approach helping the prospects of a QB wanting to get prepped for the league. In the NFL....it's a PASSING league. Not a spread option, run heavy one. And even if teams love your mobility, they DO NOT want you running a lot. Too much money on the line.
Colin Kaepernick was overlooked largely because he came out of a Pistol offense, even though he had the best size/speed/arm strength combination of any QB in that 2011 draft. Better than even Newton.
He was an Academic All American (so character was not an issue, like it was for Newton), and had a high completion percentage. Also held an NCAA record for most yds passing and running in his career.
Since he and Newton have proven to be successful in the league, it has broken that stereotype to some degree, but teams still frown a bit on QB's coming out of run-heavy systems.
Butch's system is much closer to a Pro-style offense, while still utilizing the QB in the Read Option a portion of the time. It's more like the 49'ers offense with Kapernick at the wheel.
The QB will run about 10% of the time in CBJ's system. Whereas the percentage is much higher in Malzahn's. So, Malzan might try to put on a slick sales pitch, but the stats don't lie.
That's not to say a QB like Mariotta, from Oregon, can't get drafted because he, too, comes out of a run-heavy system. But the low percentage with which OR and AU pass, is enough of a concern to GM's and scouts, when they try to make a determination if that player can translate their game to a more traditional, Pro style game.