Interesting.
I have a Sony 65X9300D TV, and used to just send it 1080p from MC and let it do its thing to upscale to 4K.
I have now switched to using madVR upscaling via MC using MC switching, and on low-quality source material noticed a "softening with noise" effect on the image. But I haven't tweaked madVR significantly, and I'm just using Jinc upscaling at the moment.
Overall though, I would have to say that the image quality is about the same, or I've just gotten used to the differences. What the TV can do is pretty amazing, but the GTX 1060 and madVR seem to pretty much match it.
Image quality is such a can of worms and so subjective in some ways. Personally, I just like to enjoy the story, as long as the image quality doesn't noticeably distract from the viewing.
One thing I do see on my Sony is that occasionally, and I mean infrequently with no obvious cause, the TV will sort of have a little glitch and then display the resolution info banner again, confirming 4K and the fps being displayed. I am sending the video signal via HDMI directly from the GTX 1060 to the TV. I'm thinking it might be a HDMI issue, possibly with the Sony. Does your Sony do that at all?
PS: I also use Scaling By Application, but that was to get Theatre View to correctly scale and not be oversized.
Windows has still dropped into "3D mode" a couple of times when I have been fiddling around, resulting in Theatre View being rendered in 1920x1080 and hence oversized. I've needed to turn that feature in the Windows Display Settings to get Theatre View back to 4K and correct sizing. Even a reboot doesn't fix that issue, as Windows retains the setting. Basically, it appears that Windows and the nVidia driver can still get out of sync with respect to the 3D setting; Windows thinks it is in 3D mode (or should be), but the nVidia driver knows it isn't playing 3D content, and so has switched that mode off. That has been improved in recent nVidia drivers and Windows updates, but it still isn't perfect.
PPS: I used to output everything in 60Hz 1080p, which meant the GPU was loaded doing the frame rate conversion. As I have now changed to custom MC display switching, as per the thread linked to above, my GPU is less loaded and I can muck around more with madVR settings. I could have used madVR switching, and played with that for a while, but found MC display switching worked better and as it is recommended, I've stuck with that. Less CPU/GPU load, less heat, less noise, more upside for advanced processing. All good.