Hi,
Yes, SLR lenses all have significant distance between outlet pupil and sensor, SLR lenses don't used to be problematic.
The cover glass is not the only issue. As the pixels have a certain depth, oblique rays may be able to reach the photo sensitive parts of the sensel. That causes shading effects, and for some reason also colour shift. In addition the oblique rays may cross over to other pixels, so say a part of green light hits the red pixels.
To that comes the microlenses, which are designed to work bet with some outlet pupil distance.
Leica has gone a long way to support their M-lenses. They developed a sensor with shallow wells and microlenses that work well with different beam angles. In addition Leica uses very thin cover glass, 0.8 mm in the M9 but only 0.5 mm in the M8. Most other makes use around 2 mm while 4/3 uses 4 mm.
Leica also has coding on the lenses and guesses aperture. This is used to make an automatic correction of colour shift and vignetting. Leica M-s would have major issues without these optical corrections.
Sony A7r have been modified to be more compatibe with Leica M glass, using thinner cover glass. But, Diglloyd who has tested this found that some A7 native lenses lost a lot of corner performance with the thinner Leica cover glass.
This, is a complex issue. In reality, the optical glass in the light path needs to be taken into account in the lens design. But in general, "biogon" type lenses will not play well digital sensors, especially not with small pixel sensors.
This video is quite informative:
http://petapixel.com/2014/09/21/video-fascinating-lens-design-101-interview-zeiss-master/
You can check this inf from Carl Zeiss on the issues:
http://lavidaleica.com/assets/reviews/zms/en_CLN41_Nasse_LensNames_Distagon.pdf
The issues are discussed on pages 11-13.
Best regards
Erik