With different electrodes it's a bit more complex, as a current in principle can flow even at zero bias. However, this current should build up an interface dipole layer to counter the different in work function, so that no current anyway doesn't flow at zero bias.
But the whole concept of workfunction is something you don't need in ATK because we treat the atoms as atoms, without any existing knowledge of their properties. We compute these properties instead. The whole Fermi level alignment etc is automatically done inside the calculation.