You are right, my answer is no. Though NR1200 has volume control for subout, its settings are in the Subwoofer Option menu. Because NR1200 HDMI input supports only 2ch-PCM, there is no way to control subwoofer volume dynamically via HDMI, unfortunately.
I have since read the service manual of the NR1200's un-identical twin, i.e. the Denon DRA-800H so now I know it does have the same volume control IC, using one of the available 8 channels on the IC. It also has it's own DAC, the AK4458, but obviously that has been changed to the PCM1690 DAC (not sure if some has the PCM5102A) IC after the AKM factory fire.
So, we are back to the first square about some of the inconsistencies of the results and your previous suggestion that:
Unlike the output of the preamp, I believe the primary use of the NR1200's pre-outs is for output to the subwoofer; when the DAC output is passed to the amplifier within the NR1200, there will be no unnecessary gain control, so there will be no THD+N degradation. But this is just my wishful thinking on my part.
is probably indeed just "wishful thinking.....". The fact is, based on the NR1200's preamp/dac block diagrams will be the same as that of the DRA-800H, it is a Marantz, costs more so it has got to be at least as good right. In that case, the subwoofer output channel is independent, ie. has it's own volume control and DAC.
Regardless, it did perform well on your test bench, good enough I felt confident to purchase the AVR-X1800H that has very similar preamp/dac section and since it is on sale for about US$500, it is good for my use as a 2Ch stereo device and expect good results. So far, it performs very well, near silent even with volume at maximum and I could not detect any distortions. It probably would measure a few dB better in terms of SINAD anyway, than the NR1200, as it has pre amp mode, though lacking the differential doc implementation that the NR1200/DRA-800H offers.