So lets start out by saying that a 50mm 1.4 has DOF at 12ft of about 17" assuming a full frame body. you could be within +-3 or 4 AFMA and still get pretty sharp images. Dot method might have gotten you there or it might have just got you close within the acceptable DOF. Either way for you that would be good because your images are sharper.
Where the method breaks down is when we start using long telelphotos where exact AFMA is more critical such as when your DOF is 6" or less wide open. Off by 1 AFMA will give you soft images with an occasional in focus shot.
As I described earlier every lens has it's own unique characteristics too and if you are looking for exactness and not just getting you close enough, then you need to use a 3D target such as a lensalign or some other targeting and measuring system to, if not make the proper AFMA selection, but to at least verify that you have selected the best AFMA for your lens/camera combination.
The photos with the 50mm 1.4 are significantly sharper now that i found its "sweet spot". I knew that the 50mm 1.4 wasn't the sharpest lens wide open and i thought this would be normal, but now the photos have a good sharpness even wide open.