As a qualified SIC, and as a required crewmember, you are "operating" the aircraft within the meaning of FAR 61.51(g). Therefore, as the SIC operating the aircraft "solely by reference to instruments under actual or simulated instrument flight conditions," you would log that time as SIC flown in instrument conditions.
You're misreading that....It says as the SIC "operating", meaning the pilot flying, that you can log instrument time. He cannot log the instrument time when it is the PIC's leg, only instrument time when it is his leg. It even says in your quote, "as the SIC "operating" the acft>>>>>>>"