The optical filter pack over the sensor has an influence on the image sharpness; it is why Leica went with a very thin cover glass on the M9: to preserve sharpness. See a suggestive but inconclusive exploration of that idea in Nikon D800E vs Canon 5D Mark III: the Nikon D800E Optical Low Pass Blur+Unblur Filter Pack.
But the core issue is chief ray angle sensor to the sensor: a short flange-to-sensor means a steep ray angle. Hence a telecentric lens design is needed in order to make the ray angle more friendly to the sensor. Even lenses newly designed for the camera will still be challenged in this regard, at least if the lens size is not to be too large. Therefore, I expect the A7/A7R to include micro lenses akin to the Leica M sensors, and to include color shading correction.
Adapting telecentric designs such as the Zeiss 15mm f/2.8 Distagon and Zeiss Otus 55mm f/1.4 Distagon can be expected to deliver high performance because the ray angle is digital friendly (unusually orthogonal to the sensor). This is generally true for all DSLR lenses, which inherently have a long flange-to-sensor distance (because of the DSLR mirror box).
Leica M and Zeiss ZM lenses on NEX?
Leica M lenses (particularly wide angle lenses) suffer from ray angle and color shading issues even on the Sony NEX-7 with its cropped APS-C sensor (2/3 the dimensions and half the area of a full frame sensor). With Leica digital cameras, Leica mitigates this with a custom sensor having microlenses.
So the question on a full-frame NEX would be whether (a) the sensor cover glass is friendly to the ray angle (thick cover glass is a bad thing), and (b) whether there are micro lenses to avoid severe ray angle and color shading problems. I would expect Sony to minimize the thickness of the sensor cover glass, and to have micro lenses also.
The camera can include software adjustment (lens correction) to correct-out color shading issues. But that cannot fix sharpness losses from ray angle.
Whether the accommodation at the sensor is enough for 18/21/24/28mm Leica M lenses is an open question, since even Leica M cameras show substantial color shading there.
I’ll be testing Leica M lenses on the new NEX (but note that Zeiss and Leica lens tests go into their respective guides, regardless of camera platform).
As shown below, color shading with the Zeiss 21mm f/4.5 C-Biogon is a worst-case due to the extreme ray angle to the film plane (sensor). For black and white conversions it is not an issue and the lens stays quite sharp to the corners on the Leica M9 or MM.