The physical capabilities of a reconfigurable assembly system (RAS) increase the agility and responsiveness of the system in highly volatile market conditions. However, achieving optimal RAS utilization entails solving complex optimization problems effectively and efficiently. These optimizations often define homogenous sets of problem instances. While algorithm configuration in such homogeneous contexts traditionally adopts a “one-size-fits-all” approach, recent studies have shown the potential of per-instance algorithm configuration (PIAC) methods in these settings. In this work, we evaluate and compare the performance of different PIAC methods in this context, namely Hydra—a state-of-the-art PIAC method—and a simpler case-based reasoning (CBR) approach. We evaluate the impact of the tuning time budget and/or the number of unique problem instances used for training on each of the method’s performance and robustness. Our experiments show that whilst Hydra fails to improve upon the default algorithm configuration, the CBR method can lead to 16% performance increase using as few as 100 training instances. Following these findings, we evaluate Hydra’s methodology when applied to homogenous instance spaces. This analysis shows the limitations of Hydra’s inference mechanisms in these settings and showcases the advantages of distance-based approaches used in CBR.