yeah, I am no way a electrical engineer, or an expert on grounding an engine, but I think back to 8th grade or something and "the path of least resistance" comes to mind. The reason I would use one bolt on the intake manifold is that it seems that the current from your valve cover and alternator will travel to your first bolt, then travel through your IM and then to neg battery. So! why not cut out that step, use one bolt, and send it straight to neg battery ground. The reason for stacking the wires is that the current will flow directly from valvecover ->alternator->IM->neg battery ground. instead of the possibility of traveling throughout the IM first.
This is all theory, but it seems semi logical to me. Please correct me if I'm wrong! Hope this helps everyone!