Recent high-precision neutrino experiments have significantly constrained extensions of the Standard Model based on additional sterile neutrino states. In particular, the MicroBooNE experiment has excluded light sterile neutrinos as an explanation for the long-standing short-baseline anomalies at the 95% confidence level. These results motivate renewed investigation of alternative mechanisms capable of modifying neutrino oscillation phenomenology without introducing new propagating degrees of freedom. In this work, we develop a framework in which neutrino masses and oscillation phases emerge from geometric and dynamical phase corrections associated with structured spacetime and open quantum system dynamics. Building on a generalized phase evolution formalism, we show that small, energy-dependent geometric phase shifts can reproduce key features of observed oscillation data while remaining consistent with all current experimental bounds. The approach preserves the three-flavor structure, introduces no sterile states, and leads to concrete, testable deviations in long-baseline experiments such as DUNE and JUNO.