It makes a difference in the phase of the waveforms outputting each pickup. Outer coils will give a greater phase shift, as the two pickups sense the string movement from locations farther apart than inner coils. This causes different groups of frequencies to add constructively and destructively. I'm sure someone here can describe the tonal effects in detail.
In any case, the tricky part is choosing the right combo of coils to humcancel.
If you were doing two humbuckers only, you would want the coils in each pickup RWRP, so that the inner coils or outer coils would humcancel together. With the added middle pickup, however, you would want the inner or outer coils to have the same magnetic and electric polarity so that either pickup can humcancel with the middle pickup when split. I have no idea whether DiMarzio does their neck and bridge pickups with the same polarity or with RWRP coils, but depending on the pole piece style and winding of each coil, you can flip a pickup 180 degrees to make either the north or south coil have the same polarity on both humbuckers, so that both pickups will humcancel when split and combined with the middle pickup.
Depending on what DiMarzio chooses, you could have a diagram for inner, outer or north-only coils, but you can swap leads on the switches and possibly rotate a pickup to get either inner or outer coils, or both north coils, or both south coils.