The whole process of using such software seems such an exercise in spurious precision...
Perhaps. However, AFMA affects every AF shot you take, so doing it incorrectly can be problematic. I've run across many people who have done AFMA incorrectly (e.g. testing at the MFD for a lens commonly used at a much greater distance).
Honestly, it doesn't matter how you arrive at the correct value for your lens(es), as long as you do arrive at that correct value. Sort of like driving a car with a manual transmission vs. automatic - both will get you there, but if you don't knw how to drive a stick shift, you're in for a jerky, bumpy, gear-grinding ride.
Actually I think there is no correct value other than the one you need at the distance you are shooting, the light intensity you have, and the type/color/temperature of the lighting on game day. Even ambient temperature can change your afma. To say there is an absolute correct afma setting for all circumstances is a bit of a stretch.
I've also seen some canon lenses straight out of the box that will not focus at infinity if you afma using the FoCal guidelines. Surely you could find one out of a batch that needs adjustment but I've seen it with several copies on different lenses. Could be bad lens design but the variability is there. You need to afma at different focus distances and choose the correct one for your shooting conditions....or just keep a notebook and switch your settings when doing close ups then landscapes.
Wether or not you trust focal to get you that optimal afma setting, it will reveal these inconsistencies so you can decide wether to sell or return that new lens for something else.