The study of subtle effects on transport in semiconductors requires high-quality epitaxial structures with low defect density. Using hybrid molecular beam epitaxy (MBE), SrTiO3 films with a low-temperature mobility exceeding 42,000 cm2 V-1 s-1 at a low carrier density of 3 × 1017 cm-3 were achieved. A sudden and sharp decrease in residual resistivity accompanied by an enhancement in the superconducting transition temperature were observed across the second Lifshitz transition where the third band becomes occupied, revealing dominant intraband scattering. These films further revealed an anomalous behavior in the Hall carrier density as a consequence of the antiferrodistortive (AFD) transition and the temperature dependence of the Hall scattering factor. Using hybrid MBE growth, phenomenological modeling, temperature-dependent transport measurements, and scanning superconducting quantum interference device imaging, we provide critical insights into the important role of inter- versus intraband scattering and of AFD domain walls on normal-state and superconducting properties of SrTiO3.