The big difference was hit in the post above. The NFO in the S-3 and the C-12 was acting as a pilot with a set of controls. They were a required crew member that underwent initial training to fulfill that position. I think they should be allowed to log sole manipulator and SIC where applicable. They are not and should not be part 1 PIC though.
Sitting in the back without a set of controls...not a chance.