The issue may be that on chip phase detection is not inherently accurate. It likely also has to be calibrated and adjusted. The tiny dimensions involved have tolerances as well, a millionth of inch error could be significant.
Have you seen anything that indicates that the onchip phase detection is inherently accurate? Does Canon have perfect dimensioning with zero tolerances? I've wondered if averaging over many sensors would mean that errors mostly cancel out, but its also possible that if they all have the same error that errors in dimensions would be additive.
Unless someone has found a white paper explaining the accuracy, I assume that onchip AF has errors as well, but I hope not.
Its certainly possible for Canon to have a utility to adjust phase detect AF by comparing it with contrast detect, so there is nothing new that way. Of course, contrast detection can have errors as well, as some have discovered.