I tended to use 25-30X due to space limitations. When good weather came, I went outdoors and needed the larger target for 50X and FF. As you noted, the 50mm f/1.4 is difficult to adjust, I also had difficulty with my 100mmL. The best was my older 300mm f/4L, it was almost flawless very consistent and "0" AFMA on all my bodies.
Same issues or worse for my Nikon D800 and 24-70mmg. Some lenses are not as good as others, but I do not know if its a individual lens thing or a lens model thing, except that I recall hearing that the 50mm is far from the best to calibrate.
I have a couple new bodies now, and have not yet decided about keeping them, so I need to do it all over again. I'm waiting on the mirrorless to decide if it is a fit for my use. I have a 7D, 5D 2, and 1D MK IV and only want to keep two bodies. I do not plan to buy another 5D MK III or 1D X unless there is a significant price reduction, or at least a fix for the black AF points.
Thanks for the heads up on the 50mm..I have that lens but have not had time to calibrate that one just yet. Good to see you are using multiples of 25x-30x as 50x can be a stretch especially with a 400mm prime or higher and space limitations. That one would more than likely have to be done outside. Speaking of the black AF points, I've not had that hinder my photo shoots as of yet though I did express concern via Canon support awhile back and as we know, no news on that as of yet or at least that I am aware.