In automated production lines, process automation devices with high individual availability are rigidly interlinked. The resulting risk of interlinking losses is minimized by decoupling buffers, offering more flexibility by the cost of additional space. Instead, flexible production concepts with more degrees of freedom could be enabled by applying intelligent control systems. To optimize and control industrial autonomous production systems with different classes of changeability, IT system architectures are required that can support strategic design as well as tactical and operational control decisions. Agent-based modeling and simulation can be used to implement the concept of a digital twin for applying intelligent planning and control. The findings on the interactions of individual system components can support planners in the design of production systems and can also be used as a basis for optimizing decision-making behavior in operations. In this paper a simulation study is conducted, in which an agent-based system architecture is applied to control an automated production process in a body shop embracing the different degrees of freedom for altering scenarios. The results show a robust production by enabling a different production concept with reconfigurable static robot cells connected via flexible mobile robots. Whilst reducing the number of production resources and buffer capacities in comparison to rigidly linked scenarios, productivity could be improved. In addition, the integration of the reconfigurable system with more flexibility into an automated production line increases the availability and thus the productivity of the overall production line.