In video yes, the 5d3 has better low light capabilities, but not in photos. The d800 does line skipping on video, so, by not using all the pixels on the sensor, doesn't have the same performance in low light as in stills. but bear in mind that like giostrante said, canon and nikon have different iso values. and the reason they used noise reduction software in post to compare the two it was because canon does noise reduction on files even before they got to the card. after 3200 and 6400 canon video files start to become really soft, unlike nikon that retains all information, so by doing noise reduction in post on nikon files you can have a more fare comparison.
For me, the d800 will always have the best pictures, and comparing the video from the internal codec's. Nikon has more sharpness and dynamic range, canon has better low light, yes, but all cameras need light, so if you give them light or fast lenses the difference in iso start to be less important. raw video it's a different story.
btw, nikon has fixed the "green tint" lcd by firmware update, and if you complain about the hassle of ultra-large files, I don't even now why are you talking about raw video on the 5dmark3.