The cost is tiny. A new program ..nothing more. Seen it done dozens of times. That's the whole point of CNC machines. If you have the machine capable of doing the work, the program is all you need and a few jigs that can be made in a day. Everything that is manufactured is made this way now. Nothing can be dome by hand in volume due to cost and quality control...and don't try me on that subject if you want something to shit out of tomorrow
I am pretty sure that given the volume KNC won't be using automated unit assembly (PCB will be assembled by automated pick & place machines). All bitcoin hardware is relatively low volume (for now). hundreds or even thousands of units doesn't warrant automated assembly on components. BFL problem isn't hand assembly it is a) they over promised, b) they had to scrap existing design because it was over power and cooling specs, c) they have been utterly incompetent in maintaining supply chain. BFL with automated assembly wouldn't be any further along in the backlog.
KNC made a couple of good decisions. The first is that it uses a standard ATX power supply. I wish it was internal but the fact that it is user supplied is smart. Anything that can be supplied cheaper off the shelf should be. BFL on the other hand used "custom" brick power supplies for their units and multiple times ran out. The second thing is that KNC used a single design for all 3 products. All three products have the same power board, same case, same case fans, and same controller. Then each product uses the same ASIC boards and heatsinks the only difference is in the number of units.
It would be stupid for KNC to invest in some high speed automated assembly given the relatively low volumes. We are talking less than a dozen components. Hand assembly is perfect.
They may be using a CNC machine to mill the cases. But that's not going to help install the circuit boards in that case. You'd need a robot capable of grabbing the boards, placing them, screwing them down, then grabbing the heatsinks, screwing those in, and connecting the wires, and you'd need to program all of that in.
It's certainly doable. But my guess it would be less effort to hand the machine-made parts (cases and PCBs) off to humans to do the detail work of screwing everything together and connecting wires.