I don't know. As far as I can tell, it's common to sell downgraded parts at lower price points, just to be able to compete at those price points as well. In
theory they could've just dropped the price for 64GB cards, and killed all cards with less capacity -- that would at least have made more (apparent to consumers) sense than sell all cards at the same (cost+margin) price.
I speculate that as manufacturing processes have gotten better, several segments of the industry simply continue to follow the old pattern of lower performance/lower price (GBs of flash, frequency of processors) from processes that did produce "quantifiable" low yields (eg: disabled core that didn't pass q/a, unreliable flash etc).
As for re-enabling flash on lower capacity cards, I remember seeing a reference to some people being able to flash/reprogram/reconfigure SSD drives for higher capacity -- not sure about sdcards. Also not sure if that was just to alter the reported capacity, or actually enabled more flash on the drive -- I can't find the article right now.
Given stuff like:
http://www.bunniestudios.com/blog/?p=3554
It doesn't seem too far fetched that it's possible.