We create two molecular devices with superconducting junctions, using nickelocene molecules, single Fe atoms, and Pb electrodes at low temperature. We find contrasting behavior based on the coordination of the Fe atom: one device shows low-bias features in its differential conductance due to the superposition of multiple Andreev reflections (MAR) and Fe-induced in-gap states. The other reveals interference between MAR and in-gap states, showcasing the diversity achievable in atomically engineered devices with identical components.