Large language model agents are increasingly being developed to control a wide range of scientific characterization tools including microscopes and synchrotron beamlines. Research into agentic control of physical infrastructure is nascent and there are few well-established paradigms for how to engineer an agentic system. There are many choices to make when designing a microscopy agent, including the choice of LLM, the number of agents to use, agent responsibilities and delegation rules, retrieval-augmented generation parameters, and more. When designing and optimizing an agentic microscope controller, researchers not only want to ensure that the agent can correctly perform known tasks but also that the agent can generalize to new tasks that it has not encountered before. In this study, we develop a benchmark and trace-logging framework that reveals a) how different choices of agent architecture impact performance at microscopy tasks and b) the limitations of benchmarks for predicting if a particular agent will perform well on unseen microscopy tasks. The framework was used to evaluate one-, two-, and three-agent graph topologies, five LLMs, RAG and context parameters, and operational constraints across 53 microscopy benchmark tests. In total, 105 agent configurations, 1,949 individual test runs, and 49,109 RAG retrievals were recorded. Direct comparisons showed clear differences in latency, token use, cost, and failure mode between configurations. However, surrogate models trained on agent architecture and test results did not reliably predict an agent's performance on new, unseen tasks. These results show that these benchmarks are useful for qualification, regression testing, diagnosis, and direct comparison, but the current heterogeneous test suite does not support a task-independent global configuration model.

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