We have studied both experimentally and theoretically the reprogrammable spin wave band structure in Permalloy(10 nm)/Cu(5 nm)/Permalloy(30 nm) nanowire arrays of width w = 280 nm and inter-wire separation in the range from 80 to 280 nm. We found that, depending on the inter-wire separation, the anti-parallel configuration, where the magnetizations of the two Permalloy layers point in opposite directions, is stabilized over specific magnetic field ranges thus enabling us to directly compare the band structure with that of the parallel alignment. We show that collective spin waves of the Bloch type propagate through the arrays with different magnonic bandwidths as a consequence of the interplay between the intra- and inter-nanowire dynamic dipolar interactions. A detailed understanding, e.g. whether they have a stationary or propagating character, is achieved by considering the phase relation (in-phase or out-of-phase) between the dynamic magnetizations in the two ferromagnetic layers and their average value. This work opens the path to magnetic field-controlled reconfigurable layered magnonic crystals that can be used for future nanoscale magnon spintronic devices.