If you're right then the relevant philosophical question would then be, "What's wrong with these questions? Why do we feel compelled to ask them?"
I think you're basically right: the questions are misguided. But I also think it'd take some sophisticated analysis to get to the core of what went wrong. Even with your description of the mechanism in hand we would keep coming back to these sorts of questions in different forms. "Why should I do what I feel is the moral thing to do?" "Why shouldn't I oppose my moral intuition since it was created by a force that wasn't acting in my own self-interest?" "Is morality all in my mind?"
lukeprog gave a list of metaethics questions here:
Most of these questions make no sense to me. I imagine that the moral intuitions in my brain come from a special black box within it, a "morality core" whose outputs I cannot easily change. (Explaining how my "morality core" ended up a certain way is a task for evo psych, not philosophy.) Or I can be more enlightened and adopt Nesov's idea that the "morality core" doesn't exist as a unified device, only as an umbrella name for all the diverse "reasons for action" that my brain can fire. Either perspective can be implemented as a computer program pretty easily, so I don't feel there's any philosophical mystery left over. All we have is factual questions about how people's "morality cores" vary in time and from person to person, how compelling their voices are, finding patterns in their outputs, etc. Can someone explain what problem metaethics is supposed to solve?