We assess independently the impact of high-temperature substrate annealing and metal deposition conditions on the coherence of transmon qubits in the standard 2D circuit-QED architecture. We restrict our study to devices made with aluminum interdigital capacitors on sapphire substrates. We record more than an order-of-magnitude improvement in the relaxation time of devices made with an annealed substrate, independent of whether a conventional evaporator or molecular beam epitaxy chamber was used to deposit the aluminum. We also infer similar levels of flux noise and photon shot noise through dephasing measurements on these devices. Our results indicate that substrate annealing plays a primary role in fabricating low-loss qubits, consistent with the hypothesis that substrate-air and substrate-metal interfaces are essential factors limiting the qubit lifetimes in superconducting circuits.