The issue that makes AFMA difficult is understanding the limitations and issues with phase detect autofocus. The concept is simple, just adjust your camera body so that it focuses either closer or further away. You can adjust it in small steps.
However, there are some pitfalls.
1. The Target. In order to adjust the AF accurately, you must be certain of the point the camera focused on, and that can be a challenge, since the camera AF system does not always focus where the little red square indicates. Targets specifically designed to assure that the camera grabs focus at the right spot will eliminate the issue.
2. Light Levels. The AF system has a lot more variability in low light. In very bright light, it will not have as much, but its always there, so take several shots and ignore the outliers.
3. Detail in the target can affect the Focus, the AF system generally prefers horizontal lines and will grab those rather than vertical ones.
4. Light color also affects AF. I don't know why, but perhaps its due to the lens.
5. Vibration. You can't detect the best focus if vibration is present.
6. Lens variability. Always start your autofocus at either the mfd or infinity. This will help with lens variability, but some lenses like the 50mm f/1.8 never quite focus at the exact same point.
Software like FoCal takes those things and more into account, even so, its not perfect.
That's not to say that adjusting the AFMAS by trial and error or dot tune is bad, it is going to improve things in most cases, but may not provide a optimal setting.
The final thing to consider is that a error of +/- 3 points is probably not going to make much of a difference. That's because AF does not change much.
Here is a curve from Focal that shows this. The curve is pretty flat near the center. You can see that just keeping the lens set to "0" is not going to make a big difference, even though -2 might be best.
Here is the curve for my 85mm f/1.8. A adjustment of -9 or -10 was definitely a improvement.