Troi might have seen the two Rikers as interchangeable had she been there when he was duplicated. The years of divergence in their lives made them different people. What if, right after Spock's death, Kirk went to the transporter, called up his last transport and worked some magic to rematerialize him from an earlier 'save state'? Or if he took the body to Exo III and had an android duplicate of Spock made? Would things really have been much different to after Spock's rebirth and resurrection at the end of III?