Hi Yapper, as far as my conversation with Leica NJ went was this. They said for me to ship in the M9 along with all my lenses. Like you, I was concerned that MP would not work well after that with the calibrated lenses. Leica NJ told me that the M9 was just to check that the body was in calibration, but most of the time, it was the lenses which were off calibration. They sent the M9 body back within 14 days. The lenses needed a lot more work to get to calibration, and cost me a bomb as some parts had to be swapped out, but supposedly my focus would be more accurate with my MP after calibration.
if it's not then I have to send my MP in, but apparently all my lenses are off and not the M9, but film was just more tolerant to there variance and maybe that's why i have never noticed it before. Also, when it comes to film, we're probably a lot more forgiving if it's not tack sharp because we'll say, oh it's the scanner, I made a mistake.....No such thing with digital with it's instant feedback. Also, I knew for awhile that my 50 summilux was already front focusing a little even on my film body but it was tolerable for me. I'm now really looking forward to the sharpness put out by the calibrated lens on my MP. My 90 AA is now scary sharp on the M9.
Hope I answered your question.