I'm more familiar with Dell servers that often stipulate special blank covers must be fitted over other blanks that may be filled by parts not present (esp Hard Drive Bays/PSU's) for thermal issues.
It wouldn't surprise me if the people who designed that server did some complicated analysis of airflow, and the results made them decide to supply a whole processor/heatsink blank to ensure a predetermined amount of airflow over the rest of the components.
Edit: Unless they were just trying to make life easy for a newbie who had never seen a 2nd CPU slot on a motherboard and didn't know where to fit the damn thing.