The article presents the problems connected with the performance evaluation of a flexible production system in the context of designing and integrating production and logistics subsystems. The goal of the performed analysis was to determine the parameters that have the most significant influence on the productivity of the whole system. The possibilities of using automated machine tools, automatic transport vehicles, as well as automated storage systems were pointed out. Moreover, the exemplary models are described, and the framework of simulation research related to the conceptual design of new production systems are indicated. In order to evaluate the system’s productivity, the use of Overall Equipment Efficiency (OEE) metrics was proposed, which is typically used for stationary resources such as machines. This paper aims to prove the hypothesis that the OEE metric can also be used for transport facilities such as Automated Guided Vehicles (AGVs). The developed models include the parameters regarding availability and failure of AGVs as well as production efficiency and quality, which allows the more accurate mapping of manufacturing processes. As the result, the Overall Factory Efficiency (OFE) and Overall Transport Efficiency (OTE) metrics were obtained. The obtained outcomes can be directly related to similar production systems that belong to World Class Manufacturing (WCM) or World Class Logistics (WCL), leading to the in-depth planning of such systems and their further improvement in the context of the Industry 4.0.