I don't know exactly how you ran the simulation - I suppose it can work sometimes (and for 2d/3d systems generally better than for 1d). The problem is of course not that it's unphysical to apply a finite bias to a perfect system, but that the algorithms in ATK are designed for the non-perfect case, because there needs to be a place in the structure where the finite voltage can naturally drop. So, the most correct result you can hope to obtain is the linear response current based on the zero-bias transmission, which you might as well compute from the bulk system, rather than wasting time on the full device calculation.