I spent a few hours today getting up to speed with it, it is a beta, so there are a few quirks. I had difficulty with both my 100mm L and 85mm f/1.8 with consistent AF results, I had similar issues with those lenses on my 5D MK II and 7D.
I calibrated my 35mmL, 24-105mmL, 50mm f/1.4, 85mm 1.8, 100mmL so far. Tests after the cal show razor sharp images.
I am planning to calibrate the long zooms tomorrow, since the setup is different for them.
They have added a lot of new features such as calculating the sharpest aperture of your lens, dust analysis, etc. I did not get into those yet.
Because they have not yet received the SDK for the MK III, you must manually enter the AFMA settings into your camera before each series of exposures at that AFMA. You get onscreen guidance, and a error message if you do it wrong.
For zooms, set your lens to wide or telephoto and it will recognize the setting and guide you to run the AFMA and set it into the body . Then, zoom to the opposite extreme and run the AFMA again, setting the result into your body. I did this again after setting both to see how much interaction there was. I received the same result at wide the second time, so there is very little interaction at wide after setting the telephoto. I did not have to set a large AFMA value, so it might be different if you set wide to -10 and tele to +17. I'd then run the wide again with tele to +17 and see if it changed.
Even having to set AFMA manually, it still goes pretty quickly once you get the setuo and process down pat.