The term "ballistic" is somewhat ambiguous. In our NEGF mode it's taken to mean the opposite of diffusive (as in "ballistic transport", below the mean free path, i.e. no energy relaxation from phonon scattering), since we include scattering of interfaces, defects, surface roughness, etc as created by any atom not in a perfectly periodic arrangement. In some other models i's defined it as "no scattering at all", which would only be possible in a perfect crystal, and thus is rather uninteresting in an atomistic picture, but makes sense in higher-level models when you only use the mobility or set transmission to 1 to model a ballistic conductor.
No matter the bias, the transmission spectrum is computed including the effects of all atoms present in the system.