How are you measuring the velocity difference? If you are using one of the higher end radar guns and getting the velocity at close to release then the aerodynamics make absolutely no difference. It is probably just a matter of which pitch he is more comfortable throwing.
I've seen a study which purported that there should be no significant difference in drag between a 2 seam and 4 seam fastball. I don't know if this is correct.
My guess is that most high level pitchers throw 2 seam fastballs slower because they are typically trying to throw the ball a bit slower whether they realize it or not. Typically pitchers try to locate a 2 seamer down in the zone and try to throw the high hard one with the 4 seamer.
In any case, unless one is measuring velocity at the plate rather than at release there's no reason why a 2 seam fastball should be slower or faster than a 4 seam fastball.
Maybe Coach Kreber could gun his pitchers and check release and crossing the plate velocities for 2 seam and 4 seam fastballs. It would be interesting to see how the velocity drops off for each pitch across a large sample. It would be pretty easy to do with a gun and a speedchek type unit.