The design of lightweight vehicle structures has become a common method for automotive manufacturers to increase fuel efficiency and decrease carbon emission of their products. By using aluminum instead of steel, manufacturers can reduce the weight of a vehicle while still maintaining the required strength and stiffness. Currently, Resistance Spot Welding (RSW) is used extensively to join steel body panels but presents challenges when applied to aluminum. When compared to steel, RSW of aluminum requires frequent electrode cleaning, higher energy usage, and more controlled welding parameters, which has driven up the cost of manufacturing. Due to the increased cost associated with RSW of aluminum, Refill Friction Stir Spot Welding (RFSSW) is being considered as an alternative to RSW for joining aluminum body panels. RFSSW consumes less energy, requires less maintenance, and produces more consistent welding in aluminum as compared to RSW. Research has shown that RFSSW is capable of producing joints of similar strengths at comparable cycle times to that of RSW. This paper presents a manufacturing performance comparison of RSW and RFSSW. Using FlexSim DES, a digital twin model of a real production welding cell using RSW on aluminum was created. The same welding cell was then modelled using RFSSW. For this study, a door assembly produced by Toyota North America was selected. The fully automated weld cell consists of 9 industrial robots making 8 unique joints, totaling 85 welds per door. Using the DES model, metrics like cycle times, throughput, etc. were evaluated on a shift level and compared between the processes. In summary, this study provides valuable insights into the comparative manufacturing performance of RSW and RFSSW, shedding light on their respective strengths and weaknesses in a production setting.