In the research workflow example, what if the first set of search queries don’t return good results. If the LLM tool loop decides to refine the queries, would this be “agency”?

I'd say so, yeah. If the LLM "decides" what steps to take, that's an agent. If the flow is "hardcoded" then it's a workflow/pipeline. It often gets confused because early frameworks called these workflows/pipelines "agents".