I think the engraved "C" on the barrel is only a factor for lenses that use the external bayonet. Usually only longer lenses, as there is a lot of depth of focus to the wide angle lenses. I don't think the "C" is ever used on the internal mount 50mm Nikkors.
The incompatibility between the Nikon and Contax is driven by the thread pitch of the built-in lens mount, different for the two cameras. This is not a factor if you are using the internal mount, as the RF and the mount are obviously compatible. There is hypothetically a difference caused by the small difference in nominal focal length between the Nikon and Zeiss lenses, but I suspect that is less than the uncertainty in focusing accuracy of the average eyeball using the average rangefinder. There are some mechanical differences, as the mounting flange on the 50mm lenses are slightly different, and I find that a Contax 50mm lens usually is a very tight fit in a Nikon mount, so maybe the other way around would be a bit loose.
I suspect the above paragraph may be considered controversial, so it would be great if any optical experts out there could chime in with some quantitative info.
Now if you have an external mount Nikkor 50mm f 1.1 lens, you shouldn't use it on your Contax, but if you can afford that lens, you can surely afford an extra Nikon body or two.
Cheers,
Dez