I agree that we haven't entirely figured out how the brain works yet. So the mechanics of how all this happens must be conjectural. Plus, I'm not a neuroscientist, so I'm just laying out a big picture (a philosophical narrative that pulls some things together).

Also, as I think I suggested in the article, I'm not saying the mind is epiphenomenal, that it's causally impotent. The brain is the tool-user, but the tool can take on a life of its own, as in the placebo effect (mind over matter). There could be a feedback loop in which the mind/tool affects the brain/tool-user, if only by helping the brain carry out its choices which shape the brain/mind's environment.

As for your first point, I obviously don't think we have no knowledge at all of our true self. The brain can't know itself directly as a brain, so it models itself as the mind, and the mind greedily takes all the credit. But we've developed the scientific methods, and have collectively figured out the brain's importance. We have that anomalous autonomy, so the brain isn't so trapped.

What I'm trying to explain here, rather, is how certain illusions about the self crop up, such as in religion.