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I used to do my own AFMA, but Focal is much more accurate. The reason is that it is difficult to tell which image of two very good ones is sharpest, my eyes just can't pick it out.
You do need a careful setup, read the instructions - TWICE. Use very bright lighting, a stable tripod and vibration proof floor are needed, or learn to holld your breath for a couple of minutes
If you want utmost accuracy and repeatable test results, change the default settings to allow the software to shoot more shots at each AFMA setting. Lenses do vary from shot to shot, so taking 10 shots at each setting will result in much more accuracy. Remember, you will not get the same focus each time, there is variation, so you are working off a average.
Lens AF does vary with distance, but unless I am at MFD, its not a issue. The bell curve of sharpness versus AFMA setting is pretty flat on the top, so a few points of AFMA make only a tiny difference in sharpness. A lens has to be off by 4-5 poinnts before sharpness suffers, and then its only a smallish amount.