You can not calculate resistivity this way, so the numbers cannot be compared at all. Resistivity is measure of the diffusive transport of electrons, over large distances where phonon and other dissipative scattering mechanisms dominate. With the NEGF method, you are instead computing the coherent tunnel resistance, which in principle is zero for a perfect crystal, so in fact such calculations are in a sense meaningless. ATK is rather designed to simulate cases where you are tunneling from a metal into a semiconducting region (can be a molecule, a bulk semiconductor, or just anything that breaks the periodicity of the perfect crystal of the electrodes, or an interface between two metals/semiconductors, whatever). And so, you compute not the conductivity but the conductance, which does not take dissipative scattering into account.