Three-dimensionally printed logpile structures have demonstrated the tunability of the transverse dispersion behavior, which is relevant in the context of chemical reactor design. The current modeling study aims to further investigate the trade-offs in such structures, extending the range of geometries investigated and addressing the limitations associated with the pseudo-2D nature of previous experiments. The relative transverse dispersion coefficient and pressure drop were determined using computational fluid dynamics simulations in OpenFOAM for structures with different stacking configurations, porosities and scaling of the structures’ unit cell along the secondary transverse axis. The latter could not be varied in previous experiments, but the current results demonstrate that this limitation suppresses vortex shedding in structures with high porosity. These vortices significantly enhance the transverse dispersion. By using a staggered stacking configuration on both transverse axes, an earlier onset of this phenomenon could be realized. Importantly, operation in this regime could be achieved without an equivalent increase in pressure drop, offering a favorable operating trade-off. The findings demonstrate that at low Reynolds numbers, the studied structures consistently outperform randomly packed beds of spheres, highlighting their potential for chemical process intensification.