Magnesium body .... that might explain it.
And of course any internals will be attached to that, an inbuilt heat sink. 6D has a much newer and lower noise sensor as well. It would be interesting to compare 'warm' and 'cold' similar specced images.
My SONY A77v has an extremely low noise sensor at ambient. So much so I don't bother much with darks in many cases.
Are you not using BYE because that should give you sensor temp for each image. Highly recommended !! I bought the 450D secondhand because it was the first Canon DSLR that had liveview and support for PC control via BYE.