There is no question about the fact that 4- and 8-core classic MacPros should have a configuration with just 3 of4 RAM slots used ... So "3of4-slots-configuration is prferable, BUT:
I remember the argument why a 12-core MP would profit from 4of4-configuration:
The Xeons ar able to create a virtual 3rd core. To max that out, you need a sum of real hardre cores that you can divide by 3 so that any pair of the real existing cores can create and use a third one. if this is not...
About RAM slots used in 4-,8-, and 12 core machines..