The formation and migration of austenite-martensite interfaces plays a key role in the reversible martensitic transformations of shape memory alloys (SMAs). How these interfaces interact with the SMA microstructure is a primary determining factor in important functional properties such as hysteresis and transformation span. Therefore, successful microstructural engineering of SMAs requires in-depth knowledge of interface behavior. The rapid nature of martensitic transformations makes experimental observations of moving interfaces challenging. Molecular dynamics (MD) simulation is a unique tool which can probe the atomic-scale details of austenite-martensite interfaces as they migrate and interact with different microstructural features. While MD simulations allow access to atomic-scale mechanisms, they are limited in time scale, typically to nanoseconds. This limitation creates problems when focusing on the entire transformation process in SMAs, specifically nucleation of new phases. To trigger nucleation on the nanosecond time scale, MD simulations must be performed so far from equilibrium that their relevance to experiment becomes questionable. Here, we demonstrate new MD simulation techniques to generate energetically preferred austenite-martensite interfaces in NiTi under near-equilibrium conditions. We then take advantage of this approach to probe interface behavior under conditions relevant to experiments. Our results demonstrate how austenite-martensite interfaces behave with dramatic differences in single crystals compared to more realistic microstructures containing features such as grain boundaries and precipitates. We identify trends in interface behavior which can be utilized to inform microstructural engineering approaches for SMAs.