The estimation of production rate (or throughput) is important in manufacturing system design. Herein, we consider the manufacturing system of an automotive body shop in which two types of car are produced, and one car (engine car) is substituted by the other car (electric car) gradually. In this body shop, two different underbody lines are installed because the underbody structures of the two types of cars differ completely; however, the side body line and main body line are shared by the two cars. Furthermore, we assume that the underbody lines are reconfigurable based on an increase in the product mix of the electric car. A simulation-based meta-model, which is in the form of a quadratic polynomial function, is developed to estimate the production rate. In the meta-modelling process, we group some buffer locations and represent them as one variable to reduce the number of variables included in the meta-model. Subsequently, the meta-models have been used to optimize two types of buffer allocation problems, and optimal solutions are obtained easily.