The Contrast Detect AF system that is used in LV, unless you use the quick focus mode that flips the mirror up does a normal Phase Detect AF and drops the mirror, uses the actual sensor to determine the state of the focus. Because it is measuring the focus at the sensor plane it needs no calibration. PDAF uses a sensor mounted in the bottom of the mirror box, which has to be mounted at exactly the same optical distance from the lens as the sensor is. This is where the possibility of miscalibration comes from.
The real problem is that CDAF is perfectly accurate, but really really slow. Also you still have the problem of making the area selected from the image that is used to Af actually look exactly at the spot you want in focus. By using manual focus, and 10× magnification you can ensure that the exact point you want to be in focus is, and usually without worrying about how much contrast you have present, or it's exact orientation.