I think what makes a good pickup is commitment. All you have to do is talk to Tim to see how involved he is in this. Also if you speak with Ray or Steve, you will see that they both care and want the best sound too. There is no assembly line production here. It is like the old Aston Martin where they would have one guy build the engine for you! You really are getting a hand made product.
Also, Tim uses the absolute best components for the job. At this point I think the only other thing that BK could source themselves would be to grow the trees that the spacers are cut from! Though I think that if using a more modern piece makes the pickup better without affecting the sound, then they do it. This is why they have cloth winding tape, rather than paper (though they can do paper for vintage rewinds). Tim has experimented and found it doesn't affect the tone and it is more durable.
There never seems to be a cost issue in the parts used either. He has scoured the world and had things built exactly how they were when the original pickups were made, even down to the braided wire and the pole piece screws. I can see how PRS pickups have made changes over the years which seem to be for cost savings (and I can really hear it too). The old pickups had N/S base plates, but the new ones are brass, which seems to dull the sound (though I am sure there is more to it than that).
Anyway, sorry that this is so long, but I was just trying to say that the real difference is dedication to making the best.