Lloyd has been looking into this, comparing the Pentax 24 mm with the Zeiss 21 on A7r, and also Pentax 90 mm with Otus, i think. I am not sure about the outcome, but I felt he preferred the smaller formats.
The other side of the equation is that the weakness of 135 lenses you mention seems to be mostly in the corners and corners are mostly not the most important part of the image. Also, new lenses are coming from Sigma and Zeiss offering much improved performance across the field.
The third part is that there is a need of stopping for aperture on MFD, if I can shoot with DSLR at 5.6 and need to stop down an MFD to f/11, diffraction will affect the MFD while the DSLR is still in the optimal region.
I would also say, that all these may be pixel peeping differences, quite visible at actual pixels on screen, but this not the way pictures are normally presented. Pictures are either shown on screen. Which has two megapixels, or in prints.
Either way, low frequency detail will dominate over microcontrast.
The opposite may actually be true. My experience with MF format lenses, although not directly from Pentax, is that they are much, much better than what is generally available in 24x36.
The reason is actually quite simple: MF lenses are generally bigger than their 24x36 counterparts (even when counting the difference in coverage) and slower. The optical engineer does not have to optimise for size or aperture.