A lens may bias the AF system due to mechanical considerations. Think hysteresis and mechanical lash. There is also an element of compliance to specification for the AF drive. Longitudinal chromatic aberration may also bias the AF system. I am not sure, but I believe that most per-lens AF calibration is an attempt to account for the last two points.
As for how the PDAF system works...the system does not detect an OOF condition so much as it finds the best phase match from its array of sensors. In other words, it seeks until it finds. There used to be an excellent applet out there that gave a very easily understood demonstration of AF in action...now if I could only find the link
In regards to carrlangas' and others comment...yes, focus shift with stop-down does happen and yes, it may throw off critical focus. In practice, this is usually acceptable within the precision of most AF systems** and is mostly a problem with critical manual focus cases. I have personally seen it when doing stop-down work using a split image and certain legacy lenses.
Steve
* PDAF is the AF system used for viewfinder photography with an SLR. CDAF (based on detected contrast) is the AF system used for live view. CDAF is intrinsically more accurate and more precise than PDAF.
** The AF points for most PDAF systems have a working precision equivalent to a f/5.6 aperture. The better systems have at least some of their sensors optimized to f/2.8. The Pentax K-3, for example, has three f/2.8 center points. Previous Pentax models have f/5.6 detectors only. Accuracy of PDAF systems for critical focus with faster lenses is sort of a cruel joke as a result. Before leaving the subject, it might be good to note that the precision of microprism focus aids in most manual focus SLRs have a similar f/5.6 limit.
---------- Post added 03-27-14 at 12:02 PM ----------
Originally posted by stevebrot ...now if I could only find the link
Found it! It takes awhile to load, but it is only too cool when it does. The accompanying lecture notes are also one of the best descriptions I have read as well.
Autofocus: phase detection
Here is the corresponding applet and discussion for CDAF:
Autofocus: contrast detection
Steve