I think you may pay more for certain colours because they have to set it up for you. If they can put your bike in with another bigger order and spend an extra two minutes doing your bike, rather than having to spend 30 minutes setting up the process just for your bike, it would be cheaper. The savings isn't in the actual powder coating, but in the setup time, I suppose.

That's my thought on the matter anyway. I just know that I was told it would be more if it was a colour that they were only doing for me.