Amazing if it all works out. I would vote for a custom color. I am torn among Pelham blue, Cardinal red, Heather or Gold. I would think these would be a tad flashier than sunburst, and if you are going to do a very limited run, then go custom color. Plus if ageing is an option, you could green up the blue easy.
I would think that if they are only doing a dozen, then the price will be nosebleed section, so what would be the difference between two or one pup? If I were going in hock, then I would go in hock for an extra pup. They can't possibly jack it up that much, could they?
I would go for whatever pup as long as the holes and rings are right, (and it has a Dasson bridge). They you could swap the pups for whatever later.