We examine the long-term evolution of accretion tori around black hole (BH) remnants of compact object mergers involving at least one neutron star, to better understand their contribution to kilonovae and the synthesis of r-process elements. To this end, we modify the unsplit magnetohydrodynamic (MHD) solver in FLASH4.5 to work in nonuniform three-dimensional spherical coordinates, enabling more efficient coverage of a large dynamic range in length scales while exploiting symmetries in the system. This modified code is used to perform BH accretion disk simulations that vary the initial magnetic field geometry and disk compactness, utilizing a physical equation of state, a neutrino leakage scheme for emission and absorption, and modeling the BH's gravity with a pseudo-Newtonian potential. Simulations run for long enough to achieve a radiatively-inefficient state in the disk. We find robust mass ejection with both poloidal and toroidal initial field geometries, and suppressed outflow at high disk compactness. With the included physics, we obtain bimodal velocity distributions that trace back to mass ejection by magnetic stresses at early times, and to thermal processes in the radiatively-inefficient state at late times. The electron fraction distribution of the disk outflow is broad in all models, and the ejecta geometry follows a characteristic hourglass shape. We test the effect of removing neutrino absorption or nuclear recombination with axisymmetric models, finding ∼ 50% less mass ejection and more neutron-rich composition without neutrino absorption, and a subdominant contribution from nuclear recombination. Tests of the MHD and neutrino leakage implementations are included.