That does not make any sense. "Too few levels" can only increase the intensity of noise; it does not hide it.
When you have only three levels in a stop, you see "smooth" areas.
12 bits is all that is needed to convey all the signal and analog noise in current cameras, and that is needed only at the lowest ISO(s)
I just showed above, that the lack of reduction of the 16bit values to 12bit caused noise.
Note, that this does not contradict my other statement, that the lack of levels causes the 5D images appear less noisy; in the area I used in the demonstration there were still 8-12 levels per channel after the reduction.
You can't zero out the LSBs and expect to get good results. (and you *did* do it at the grey CFA stage of the RAW data, I hope). You are clipping shadow detail by doing that, and darkening the overall intensity. You must add 1/2 ADU of the resulting bit depth in the original one first. In this case, you must add 8 before you integer-divide by 16
The effect of *maximum ONE* in the pixel value range of 1-4095 is negligable. Btw, who told you, that the value would be rounded if there were only 12 bits, instead of truncated?
The lack of black in your non-quantized +5EV P30 makes me think that there is some quirk in the processing. The image looks too pale green.
After +5 EV only the "true blacks" appear black, and those are in other parts of the image (only some edges of the wooden doors on the kitchen island show massive blacks).
Re the color: 1. I did not make any WB, 2. there is no proper de-mosaicing, only an averaging of the colors. Sometimes I turn off even that, and then the image becomes very green, because half of all pixels are green (the true sharpness of the image can be seen that way).