The MkII (now called REF1000M) definitely takes things further than the original REF1000. The addition of a custom input stage board and another board with a custom power stage make the REF1000M a different beast and hence the higher price. So, I don't think anyone can say it is just an amp with reboxed ice modules.
The following video is a little old, but it explains a lot of things. John Stronczer has the S-500 (now called the REF500S stereo amplifier) cracked open and explains the input stage and then also explains the extra power stage board which is added to the REF500M monoblocks and REF1000M monoblocks.
http://uk.cinenow.com/videos/1861-bel-canto-s-500-stereo-power-amplifier-top-audio-milan-2008
The following video is a little old, but it explains a lot of things. John Stronczer has the S-500 (now called the REF500S stereo amplifier) cracked open and explains the input stage and then also explains the extra power stage board which is added to the REF500M monoblocks and REF1000M monoblocks.
http://uk.cinenow.com/videos/1861-bel-canto-s-500-stereo-power-amplifier-top-audio-milan-2008