You are mixing up religion and meditation.

Think of meditation more as a physical exercise for the brain, like yoga. Is yoga a religion, even if it strengthens your core? Many people do it without any religious ideas.

Same with breathing, 'low CO2' sounds bad, but we do have the next breath, the goals isn't continued low CO2, it can lead to increased oxygen later.

As to rationality. Meditation helps declutter thoughts, so that helps with rationality doesn't it? Why would being strung out and stressed be more rational?