I guess it depends on what question you're asking. You seem to be pointing out that you think the real question is: "what is the median rent for anyone living in San Francisco?" whereas Zumper seems to be more answering the question: "if someone moved to San Francisco today, and has zero connections, what rent would they pay?"
Both are valid questions, but I think it's good to set the context for if you're having a conversation about "general median rent" vs "newcomer median rent."