I have not read any of the discussion on DIYaudio about the differences between the two modules. However, as a 30 plus year tweak, I can say that even the smallest physical difference can make a huge sonic difference. The power supply diodes, the power supply caps, the voltage of the power supply, the voltage and type of caps on the board, the layout, the grounding, the trace thickness, the resonance of the heatsinks and chassis, they type of connectors used on the power supply, the fuse, the fuse holder, the brand of solder, whether or not you use leds in the circuit (generally, leds mess up the sound and the NC400 has a bunch of them in it)....don't know if the 1200 has them), brand of resistors, brand and amount of output devices, whether the hardware is magnetic or not, etc. etc. etc. All the above is true. I have experienced it directly. So, any number of things can make a sonic difference. If you have not done 30 years of subjective listening tests on all kinds of things then you think that it must be something you can measure or some obvious single thing that you see. When I look at something I see a ton of things that can make a difference.
There is no doubt that the discrete stage in the NC400 sounds different than the IC in the 1200. Never heard op amps that don't have a different sound from each other and discrete circuits all sound different as well. But then there are a ton of other things that would make a difference sonically as well. Although a great discrete circuit will sound better than any opamp, a great opamp will sound better than a lot of discrete circuits not executed well.
I was wondering why the latest Oppo that I modded was not sounding that good. And then I realized that I had not put 7 cents worth of constrained layer damping material (one half inch by one inch) on the heatsink of the plus 15V regulator. So, I put it on and OMG! What a difference. The sound was transformed from a stereo to a live performance.....staggering. Of course, I did measurements before and after and after the damping material was put on it measured 10 billion times lower distortion.......not......he he. I mean, if it does not measure differently, it cannot be important......not. And naturally, all listening tests were quadruple blind (and deaf as well. he he).
When we don't know that much then we look for simple answers. Why things sound the way they do is one of the most complicated and complex things there is. I have been listening to various parts and implementations for years and I still feel like I know next to nothing. It is infinite......just like our own nature.