It actually IS demonstrably true that the brain is made of atoms. That makes it a quantum system, which our modern physics tells us how to simulate. The use of the term "impractical" here refers to the fact that we don't have quantum computers and that we don't have the computing power required to simulate such a large quantum system.

I'd say dismissing thousands of years of philosophy here is relevant, since it was likely produced before we had the tools to understand what we're dealing with. All experimental physics points towards an understanding of how quantum systems work, and that's all we need to model any quantum system. The brain is not any different because it's a brain.