We have studied, experimentally and theoretically, the effect of a layering sequence on the magnonic band structure in dense arrays of both asymmetric- and symmetric cross-section tri-layered Py/Cu/Fe and Fe/Cu/Py nanowires. The spin-wave dispersion for these artificial crystals has been measured with Brillouin light scattering (BLS) spectroscopy. We also carried out numerical simulations of the dispersion using an original model employing a 2D Green's function description of the dynamic dipole field of the precessing magnetization. The presence of the Cu spacer exchange-decouples the two magnetic layers, which stabilizes two equilibrium states of static magnetization. These are the parallel and antiparallel states, for which the static magnetization vectors for the layers are either co-aligned or anti-aligned to each other, respectively. These states are stable in a range of applied fields that depend on the layer width and their ordering in the stack. The magnetization configurations and layers sequence, as well as the presence of acoustic (in-phase) and optic (out-of-phase) spin-wave modes, have a significant impact on the magnonic band structure both in terms of the frequency positions of the dispersive and stationary modes and on their spatial profiles.