That wont be the reason for sure! For example the early 6 pots have large pistons and the later ones have smaller pistons. The smaller ones offer greater feel and no noticeable loose in performance, hence the later smaller pot ones are worth more. I have the earlier larger piston ones (but will be going pedal box with 2 separate systems and choose my own master cylinder sizes to get rid of this problem).
The mk4 boys use the 996 rears!