Despite the importance of modeling lattice thermal conductivity in predicting thermoelectric (TE) properties, computational data on heat transport, especially from first-principles, in 2D metal-organic frameworks (MOFs) remain limited due to the high computational cost. To address this, we provide a benchmark of the performance of semiempirical self-consistent-charge density functional tight-binding (SCC-DFTB) methods against density functional theory (DFT) for monolayer, serrated, AA-stacked and/or AB-stacked Zn3C6O6, Cd3C6O6, Zn-NH-MOF, and Ni3(HITP)2 MOFs. Harmonic lattice dynamics calculations, including partial atomic contributions to phonon dispersions, are evaluated with both SCC-DFTB and DFT, whereas anharmonic transport (i.e., thermal conductivity) is evaluated with SCC-DFTB only. Our findings further suggest that unlike the other stacking geometries modeled, serrated Zn3C6O6, serrated Zn-NH-MOF, and wavy serrated Ni3(HITP)2 represent stable geometries. While Zn3C6O6 and Zn-NH-MOF exhibit a higher power factor than Ni3(HITP)2 (as found in our previous work), Zn-NH-MOF shows lower thermal conductivity, resulting in the highest thermoelectric figure of merit (ZT) among the studied MOFs.