The Human Conclusion: The Physical Brain I am going to add on my point, as well as yours, because your statement above helped me think through this.
Meditation teaches you to be aware of the multi dimensions of the brain, it is the silencing of the rational brain, which we so loudly acknowledge in this society. Because it is in control and makes irrational decisions, by shutting down the rational brain you give space for the other aspects of the brain: realities, emotions, and feelings. Stick a knife in the brain and you have no more awareness, no more thought.
Meditation brings awareness to the body, it comes from your mind. Sure, your brain reaches out to your body and makes connections and further helps interpret those connections to your being.
Whether the brain extends throughout the body and beyond, it is the brain the allows, controls, and navigates all the data you receive as well as the "beyond" that you are going to. (This is especially seen in the spiritual realm of the brain I mentioned. I do not however believe that the brain is reduced to intellect, it is not just one function. I concur with you that the brain is just a tool, it just happens to be the tool that interprets you who you are. In saying that I am stating that the brain is the navigator of all the realities you are becoming aware of. Unlike modern humanistic theories that revolve around intellectualism, I, like you, see the brain as as a multi-functioning tool whether it be through the arts, meditation, or other, as relevant and or equal interpreters of reality. However it is the physical brain that interprets this, not an external source.