One important factor is full well capacity and we can deduce it from Signal Noise Ratio.
Sony A7rII and Nikon D810 have an SNR of 46.3 and 46.4 at base ISO, while the S (typ 006) has 42.4. So the Leica cannot make use of it's sensor size. The Nikon D810 and the Sony A7rII also have lower base ISO and that indicates that they absorb more light.
The only advantage the S2 or S (type 006) may hold is really MTF, due to larger pixels. But to reach that advantage the S/S2 would need very accurate focus and there is significant doubt if it can achieve it. Manual focus is not quite accurate enough and AF is problematic, too. Sony A7rII and Nikon D810 can use magnified live view for pin point accurate focus, CCD based sensors don't have that capability.
The CMOS sensor in the S (Type 007) is probably a better match. But, best of breed 24x36 mm technology is quiet a bit of very stiff competition for slightly larger formats.
100 MP at 54x40 mm combined with Sony Exmoor technology, that is a different race…
I thought to an extent this still goes back to the old adage "no replacement for displacement" or in the camera world...sensor size. Imagine drawing an image on a postage stamp and an 8x10 canvas. Which one will have the ability to show more variations of tone, subtle detail, and finer variation? Obviously the larger working space. It's just straight forward.
Does the Leica S2 show more...yes probably, it has a somewhat larger sensor surface area. (30% is it?)
The difference now a days is that tech has gotten really good. Lenses have gotten really good. Resolution shrinks the gap between the extremes.
If you have ever seen an original 11x14 contact print that was masterfully made it is breathtaking. Nothing we have compares in my opinion. Though technically it may not be as clinical, the subtlety is amazing. Talk about surface area!
Image quality is subjective. And everything now a days can create excellent prints and visual content. There is still a difference is fine variation and tonal gradation between sensor sizes. I use m43 and a 49mm my sensor daily together. The gap is not huge, but there's is a difference. There is a difference between this and my 36mm sensors going either way. But the gap has gotten inconsequential for most images for most general uses. In my opinion.
I notice the subtle tone differences mostly in skin and twighlight images..at least in the work that I do. There is more complexity and "truth to the scene" in the larger sensors. However, that doesn't necessarily make it any better.