Allow me to quote
from this site:
"Lets consider that I have a camera body that is -2 focus units from perfect, and a lens that is +2 focus units from perfect. Both are considered fine according to the manufacturers definition, although they certainly arent perfect. However, the combination of a +2 lens on my -2 camera will be absolutely perfect, Ill love the lens on my camera...
But what if the lens was -2 focus units from the theoretical perfect and I put it on my -2 focus units from perfect camera?...
... if its an f/1.4 lens with a very shallow depth of field, the front focusing will be noticeable: the subject will be out of focus and soft... if I sent the lens in to the manufacturer to fix the problem they would check the lens out, say it was fine (because it is fine, its within specifications) and send it back. Ony if I send the camera and lens together to be calibrated would the fact that the two together are out of focus be apparent, and then the manufacturer would be able to fix the calibration."
IOW, the lens calibration must match the body.
So, what you do is this: you send both the camera and lens to CSC for calibration. You tell them to ensure the camera body is calibrated to standard (they use a standard lens for checkin). You must also inform them they should calibrate the lens to match the body if the latter is within spec. While it's possible to calibrate the body to match the lens, it's not easy and CSC won't be able to do a good job (personal experience).