It is meaningless to compare the total energy of a two-probe system with the one of a equivalent bulk system or a scattering region. The reference for the zero of energy is ill-defined for a bulk system. Maybe, the formula for the total energy of a two-probe system can be found in the following paper:
M. Brandbyge, J.-L. Mozos, P. Ordejón, J. Taylor, and K. Stokbro, Phys. Rev. B 65, 165401 (2002)