So what's going on Canon 5D 2 &3 and Nikon D800

Actually you were clear;

I think the question you should ask is why the D800 shows about 1 to 2 stops greater light gathering across the board.

if this is the case then the video should be compared as follows...

ISO 6400 Canon vs. ISO 3200 or 1600 Nikon:

Based on the samples this would be the more logical comparison, after all, the purpose of the video capture is to be able to record the image, which has to be bumped up significantly in the Canon were you don't have to on the Nikon...

Also my understanding is that the update for the 5DIII will not give uncompressed video, only clean video out through the HDMI. I may be wrong however.