The difference in sound is related to position. The guy with two humbuckers almost on top of each other (eastcoasteddie) heard a lot of difference between inner and outer coils mixed - that absolutely makes sense, as the two inner coils are much closer to each other in a relative sense than the outer coils. On a bridge pickup, the difference in relative position will also be pretty big going from one coil to the other within the same pickup. For a pickup far from the bridge, the difference will be more subtle, but probably still audible if you're paying attention. Position of a pickup is one of the most important factors in the sound of a bass - that position creates a comb filter for each string that is not eq-able - it's baked in, with no way to fix it, as the eq for each string is different, and their outputs are summed in the pickups' outputs.
Well how about this: Has anyone ever mixed-n-matched Magnets so that you one coil with Ceramic and the other AlNiCo V or one AlNiCo V and the other III? I wonder what it would sound like as a humbucker and then you'd get 2 distinct single coils. Now I think ceramic PuPs run their magnets differently than AlNiCos so I dunno if that is feasible... let alone wise...