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Despite the growing presence of chatbots, few studies have explored how students exercise autonomy when offered multiple interaction modes. This mixed-methods study investigates how learners engaged with a dual-mode chatbot, general (large language model, LLM-based) and reference-based (LLM and retrieval-augmented generation-based) modes, in a large-scale online course. Based on chat logs, learning management system logs, server logs, and post-course survey data (n = 121), the findings revealed that more than 40% of students were unaware of mode choices. Those aware favored the general mode for convenience and the reference-based mode for precision. Mode selection was significantly associated with interaction behaviors and perceived learning experiences. These findings highlight the importance of learner autonomy, awareness, and design integration in chatbot-mediated learning environments.