We treat phonon transport with the McKelvey-Shockley flux method, which is efficient, captures ballistic and non-equilibrium effects, inelastic scattering, and has shown excellent agreement with the more computationally-demanding Boltzmann equation. The Si and Ge phonon dispersions and 3-phonon scattering rates, serving as input for the transport modeling, are calculated from first-principles. The results show that, while the maximum phonon frequency in Si is nearly double that of Ge, significant heat currents are carried by the high-frequency Si phonons above the Ge cutoff. When approaching the interface, inelastic scattering redistributes energy to the phonon frequencies that can transfer elastically across the Si/Ge junction. We explain how this collective reorganization of phonons is driven by non-equilibrium effects near the interface. We also include a model for the contact resistance of an ideal interface, that depends on both phonon dispersions, which provides a lower limit for a given material combination. These results help provide clear physical insights into what controls phonon transport at semiconductor/semiconductor interfaces.