The difference is more control. With automatic mapping, you have to manually set the breaking angle, and that can yield some undesirable results. I know many people who start with automatic mapping and then clean up from there, and that works for them. I, personally, like to get my UV shells set the way I want them from the get-go instead of having Maya make those decisions for me. Also, I can control the number of individual shells that get mapped initially. With automatic mapping, you can nearly as many shells as you have faces, which is very unmanageable. With my method of mapping, I can limit the number of shells.
It's all about control.