For fast lenses, f 1.8 and faster, I tend to prefer the 25X distance, but for telephotos that are used mostly on far away objects, I use 50X if I can.I'm thinking about Reikan FocCal Pro, do they provide setup distance for each lens?
You choose the distance. Canon recommends 50x the focal length, LensAlign recommends 25x the focal length (i.e. about 16' and 8' for every 100mm of focal length, respectively).
Personally, I test all lenses at both 25x and 50x the focal length (and multiple focal lengths for zooms, wide, tele and 1-3 in between), then look at the overall results to decide the AFMA value(s). It's going to be a compromise, more data drives a better decision. I take into account the subject distances with the lens (close for the 85L, far for the 100-400, etc.), the usual DoF (weight close distance more with wide lenses). It means lots of testing, which is why the automation is great.
My Canon 100mm L is a puzzle. A totally different AFMA at close distances of a couple feet or less than at normal 7-20 ft distances.