Magnetite Fe${}_3$O${}_4$ exhibits complex electronic and magnetic properties associated with its mixed-valence state and the Verwey transition. Here, we systematically investigate the thermoelectric, structural, thermal-transport, and magnetic properties of Mg- and Al-substituted Fe${}_3$O${}_4$ single crystals. Although the Verwey transition is suppressed in both systems, their physical properties exhibit markedly different composition dependences. In Mg-substituted Fe${}_3$O${}_4$, the absolute value of the Seebeck coefficient increases with increasing Mg content, and its composition dependence is reasonably reproduced by the extended Heikes formula, highlighting the role of the Fe${}^{2+}$/Fe${}^{3+}$ mixed-valence state and its associated configurational entropy. In contrast, Al substitution produces more pronounced changes in the lattice parameter, thermal conductivity, and magnetic properties, while the Seebeck coefficient and Hall-estimated carrier concentration change comparatively little. These results demonstrate that Mg and Al substitution affect the physical properties of magnetite in different ways, reflecting their distinct effects on the Fe${}^{2+}$/Fe${}^{3+}$ mixed-valence state and the different magnitudes of the accompanying lattice contraction. This comparative study provides insight into how chemical substitution can tune the interplay among electronic, thermal, and magnetic properties in correlated oxides.