Maybe I am naive but to me this is blindingly obvious:
If they measure each lens for focus shift in the factory at every aperture, then have that lens tell any S2 body on which it is mounted how much it needs to tweak focus from what AF has told it, at the precise moment of stop-down for exposure, then there is nothing going on with the image file itself, at all. Consequently the there is no trade off between requirements in image processing.
If there are compromises in the lens design such as those resulting in CA, distortion of field, vignetting, which need software correction (and I don't care whether those software corrections are pre-RAW or optional in RAW development) then there ARE tradeoffs in image quality during that processing. If you correct for vigging in software, you increase the noise in the corners because you are effectively adding exposure compensation in the corners. If you correct for sharpness falloff in corners you add noise in the corners because you add sharpening. If you correct for CA you distort colour and sharpness accuracy. If you correct field distortion you add interpolation, which is the same as upresing selectively.
So: if the S2 only does stuff to the lens at stop-down to compensate for focus shift, then I think that's really smart and it forces fewer other compromises on the lens design. But anything that requires resampling, sharpening, selective exposure compensation, whatever, IS costing IQ because it is trying to fool the eye into getting more from the pixel data.
If the S2 does notably less of this than Hassy et al (and as we all well know Phase does it too) then it will give a purer image and one that more accurately reflects what the lens projected onto the sensor. That's what I'd pay for because, frankly, I don't like using C1 to 'correct' lens failings such as the corner softness of the Phase 28D. The results, to my eye, look crude at larger print sizes off a P45+ and that means that I am not getting the best that can be got.
That is where the S2's killer value proposition might well be.
My 2 cents.