An excellent description of the AF process used by Canon can be found here
It's from a few years ago but still "current" . One paragraph is relevant for this "calibration" topic
rdkirk wrote
When you mount a lens (whether the camera is on or off), the camera interrogates the lens for its characteristics, including maximum aperture, which is one of the focusing parameters.
When you half-press the shutter release (or the * button, if you've used the custom function to move focusing control there), the activated AF sensor "looks" at the image projected by the lens from two different directions (each line of pixels in the array looks from the opposite direction of the other) and identifies the phase difference of the light from each direction. In one "look," it calculates the distance and direction the lens must be moved to cancel the phase differences. It then commands the lens to move the appropriate distance and direction and stops. It does not "hunt" for a best focus, nor does it take a second look after the lens has moved (it is an "open loop" system).
Each lens has a stepper motor that tells the camera its position (from min to max on the focus ring's range) by providing a "number". Each lens will have a series of numbers (addresses) from its min focus to its max focus distance and once the AF has calculated the necessary movement, camera is supposed to tell the lens to go to # xyz. The lenses should come from the factory with those addresses "well calibrated" to the real distances they correspond to (but it may be "off" a bit and can be reset). How well these settings correspond with the distances ( +/- some number of counts or inches or whatever) is a manufacturing variable. It is these addresses that are reset in the calibration procedure. When you do micro AF it adds or subtracts from these addresses, as you adjust the scale on the display, until you find it's right. This number tells the camera the distance now corresponds exactly.
The AF sensor also has "tolerances" in how it measures and sends its commands and these can be off slightly in a "manufacturing tolerance" range. The combination of these two tolerances is what can result in pairings that are quite "off" and also make a lens work fine on one camera but not so well on another. I think the "body" side of things is under better manufacturing control than each lens so micro AF will usually do the trick!