The retort to Nikhil's essay may have all the technical evidence of the brain being reliable, but it misses out on some of the more underlying points Nikhil was making. For one, Nikhil implies that the idea of trusting one's own brain is naive and inherently flawed due to our human nature and the fact that we are more prone to errors of judgement than machines. Despite the research cited in the retort that talks about how our brains are capable of accurate decisions, Nikhil also acknowledges that humans are still subject to biases and errors, thus leading to his conclusion that he does not have full confidence in what his brain tells himself.
Furthermore, Nikhil's essay touches upon the idea of trusting oneself, rather than simply trusting our brains. We tend to think that if our brains tell us something, it must inherently be true, but that is only true if we trust ourselves enough to make sure there are no underlying factors affecting our judgement. This is an important distinction because, as Nikhil points out, our brains can be affected by external factors such as stress or fatigue, and if we want to make sure that we're making accurate decisions, then we need to be mindful of those external factors.
Therefore, although the retort may be technically accurate, it fails to address the bigger picture that Nikhil was trying to make in his essay: trust yourself rather than blindly trusting what your brain tells you. It would be wrong to suggest that Nikhil's original assessment of his own confidence in his brain was wrong - in reality, it was a cautionary tale about being aware of oneself and one's external influences when making decisions. In other words--trust your brain, but don't always believe everything it tells you!