The great thing about shooting RAW is you can post process. On a computer with much bigger screen, you can determine the noise reduction level to balance between noise & detail. As rule of thumb, if you shoot RAW, better turn off all the in-camera processing such as High Tone Priority, Auto Lighting Optimizer, High ISO Noise Reduction, Lens Correction, etc.
The 6D's manual in the RAW sections starts with: "A RAW image is raw data output by the image sensor converted to digital data". Are you saying there is some in camera processing such as High ISO NR even with RAW? I believe that based on the results of tests I have done and what others in this thread demonstrated.
Is there a table somewhere on the web or in a manual that lists those options that impact RAW processing?
There is only one option effect RAW setting which is Long Exposure Noise Reduction because it use dark frame subtraction method. Everything else you can change in post processing. What you see on your camera LCD screen is not the actual RAW file but it is the camera-processed image. Thus, if you turn off all of the camera processing settings like I listed above, then your RAW and display JPG will be really close to each other. That way, it is easier for you to judge your photo.