I got to play a "custom shop" Snakebyte and compare it with my regular old factory ESP Snakebyte and there simply isn't a difference. The wood used might have been more expensive or something but it didn't come out in the tone or playability at all and could not be heard through the amp. Acoustically the factory was a "little" bit brighter sounding that we could all tell by ear but if you took 5 different Snakebytes...you'll hear the same differences.
I can only surmise the builders that make them in Japan get paid a metric shit-ton of money and voila....your extra $3000 is accounted for. The problem with that is that the guy sitting in the next room over is cranking out the same guitar from the same pile of wood and is getting paid starvation wages or something.
Shenanigans I tell you.