What I meant to say was, that if we want to model the real physical temperature-dependence of the current, we need phonons etc since the current computed by ATK in the ballistic regime are strictly zero-temperature results. As you noted in another post, the "temperature" used in ATK is rather a numerical trick to aid convergence. This trick may cause T(E) to depend on the "temperature", but the true result is obtained when the "temperature" is extrapolated (somehow) to zero.
(To avoid confusion on this point, it might be better not to use a temperature parameter, but rather specify the Fermi broadening explicitly, as an energy... What do you think?)