The methodology is not about testing the efficiency of the whole AF system in real life situations. It is about testing wether or not, on the simplest possible target, phase detection produces front or back focusing.
If the camera is not successful at properly focusing such a target, it's a clear sign there is a problem. You cannot hope to get good results in real life situations like you describe if the camera cannot even handle ideal conditions. It's just step zero in the troubleshooting strategy.
Here is what I would recommend to people about the whole fine tuning business:
1) Just use your camera without worrying about it. If you get a high percentage of pictures in focus, everything is fine. No need to shoot targets. Out of focus images will happen, no system is 100% accurate and the number of bad images will decrease as you will gauge better how you system behaves.
2) If you systematically get out of focus images, it is either you that has poor technique or your camera needs to be checked. If you think your technique is proper, then try a method such as the one I propose. If your camera systematically misses this straightforward target, your autofocus system is not well calibrated and you should consider fine tuning it by analysing the test pattern on the dotted chart. Then go back to real life photos and see if things have improved. The method has no other pretension.