Cardiac autonomic modulation (CAM), which is regulated by the balance between the sympathetic and parasympathetic nervous systems, is involved in various physiological and pathological conditions. Heart rate variability (HRV) analysis has been used to explore the complex relationship between the brain and heart, as described by Porges’ polyvagal theory and Thayer’s neurovisceral integration model. Recently, an automated calculation of new parasympathetic, sympathetic, and Baevsky stress indexes based on HRV parameters has been introduced for faster and more comprehensive CAM assessment, though their normal ranges remain undefined. This study aimed to determine the average values of these indexes in a healthy population of different ages during rest, daily activities, non-rapid eye movement sleep, graded physical effort, and acute psychophysiological stress. At rest, the parasympathetic and sympathetic indexes were consistently within the proposed normal range and inversely related. However, Baevsky stress index values from Kubios were higher than expected, conflicting with the assumption that they are simply the square root of those calculated using the original formula. Despite this, time-varying assessment of all indexes can provide valuable insights into CAM adaptation during physical effort and acute psychophysiological stress in real-world critical situations. Notably, our novel finding shows that the inverse correlation between parasympathetic and sympathetic/stress indexes under stress is better explained by non-linear functions, offering a potential new measure of brain–heart interaction during real-life critical events.