I doubt if there is any difference in results. FoCal has had time to make several improvements over the past 1+ years, and they now understand the limitations of AF systems much better than they did. They do still discover new things almost every week. There is a new post about discovering a bug in Nikon Firmware for almost every Nikon Camera that causes it to put the wrong AFMA value in the image metada, which, of course affects the testing.
Autofocus varies from shot to shot a lot more than we think. Usually it is not enough to notice unless you are really looking hard, but it also flat out misses.
FoCal has so much data from the thousands of tests that they can predict the correct AFMA with only two shots, the third shot being used to verify the results. They have developed a much more accurate AF algorithm than the one Canon uses in liveview, so they can determine the peak resolution of a perfectly focused lens, and then use curve fitting with two points.
The FoCal manual is available for viewing or downloading. I sat down and read all 130 some pages a few evenings ago. I learned a lot about how Canon and Nikon's AF works, and at least some of the weak points. Its worth reading about the tests you can run even if you don't buy it. http://www.reikan.co.uk/focalweb/index.php/why/documents-to-download/