6D + Canon 50/1.8 or D600 + Nikon 50/1.8? Help me decide.

like 0.5 stop better.

not fine enough. first, there is a lot of red noise in darker part of the image, hard to get rid of, second with 60D exposing this type of scene need absolute precision  you have no room error, 1/2 stop too much you lose view in the window, 1/2 stop too fast you lose indoor detail.

5 stops from iso 100 is indeed iso3200, so if a scene had so much contrast that you needed to pull 5 stops, then of course you will get iso3200 noise. it is just software amplification instead of hardware amplification.