Troy,
These are the weaknesses of your proposed system as I see it. The CLE has no framelines for your proposed 50mm, only 28, 40, and 90. It has a short rangefinder baseline, which is a problem only if you shoot with fast lenses wide open.
The number one shortcoming for me is that the meter doesn't work at all in manual mode. You have to meter in automatic mode, then remember the reading and reset the shutter speed dial, which requires that you depress an awkwardly placed release button to unlock the shutter dial. Using a separate light meter is faster for me than using the internal meter on manual mode. There is no exposure lock button in autoexposure mode. You do get +/- 2 stops of compensation on the shutter dial in 1/2 stop steps, but you have to push the awkward release button to get it. If the battery is gone, you have no camera. Luckily the batteries are the still-common SR-44 (or 357, etc.).
If you plan to use the camera on autoexposure over 90% of the time, or with an external meter, it will probably work well for you.
I haven't tried it, but I'd expect no problem with the Zeiss 28mm on the CLE. The only potential problem I can see is that the recessed lens parts might block the light meter cell in the floor of the camera from reading the shutter / film plane. I was going to suggest that you try asking Steve Gandy at cameraquest.com about the Zeiss 28mm on the CLE, but it appears that Zeiss has taken back distribution from Hasselblad, and he can't get the cameras and lenses anymore.
I'm not trying to run down the CLE. It's a very nice, quiet, discrete camera that can fit excellent optics. The viewfinder is excellent. My father bought this CLE after he had cataracts and detached retinas because he could see through it clearly and focus it better than anything else he could find reasonably priced. For flash and autoexposure shooting it's great, and I'm keeping mine. I just don't often work the way the CLE is designed to work.
Lee