I think the interesting point that hasn't been raised yet (as far as I've seen in this epic thread) is how KNC have binned their chips, if at all. BFL have 2 chips per Jalapeno and each can be (and usually seems to be) of a different quality in terms of hash rate and they must manually balance which chips get put on which board to achieve the advertised hashrate. Bigger boards have way more chips and it then becomes a classic partitioning problem.
Very good point, AFAIK, the chips are currently not binned at all. Not even tested for functioning (neither wafer probing or final chip testing) before being soldered on the PCB. Thats a huge mistake IMO, one that was pointed out months ago. They could be testing/binning the completed modules, but Ive not heard a word on that.