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Over the past decade, there has been a surge of interest in the transport community in the application of agent-based simulation models to evaluate flexible transit solutions characterized by different degrees of short-term flexibility in routing and scheduling. A central modeling decision in the development of an agent-based simulation model for the evaluation of flexible transit is how one chooses to represent the mode- and route-choices of travelers. The real-time adaptive behavior of travelers is intuitively important to model in the presence of a flexible transit service, where the routing and scheduling of vehicles is highly dependent on supply-demand dynamics at a closer to real-time temporal resolution. We propose a utility-based transit route-choice model with representation of within-day adaptive travel behavior and between-day learning where station-based fixed-transit, flexible-transit, and active-mode alternatives may be dynamically combined in a single path. To enable experimentation, this route-choice model is implemented within an agent-based dynamic public transit simulation framework. Model properties are first explored in a choice between fixed- and flexible-transit modes for a toy network. The framework is then applied to illustrate level-of-service trade-offs and analyze traveler mode choices within a mixed fixed- and flexible transit system in a case study based on a real-life branched transit service in Stockholm, Sweden.