Definitely something I would ask ben or Tim. I personally don't think a couple inches would be the only thing that changes the tone so drastically between the neck and middle pickup
Well - in my experience it really does. I have swapped neck and middle pickups to achieve the desired humcancelling combinations in at least two guitars and have not noticed a difference in tone of the individual pickups (these were not BKPs but I believe the results with BKPs would have been the same).
BTW I am not really a middle pickup player and much prefer the neck or bridge pickups.
Going by specs it appears that neck and middle pickup are the same in each SC set but in the end only the BKP team can give you positive assurance on that.
Cheers Stephan