The study demonstrates the complex two-way interaction between coffee consumption, HRV, and other lifestyle factors. For example, high levels of stress or lack of sleep (neither of which was measured in the study) might lower HRV readings, but also cause high coffee consumption.
In those scenarios, there may not be definite causal relationships between coffee consumption and HRV.
In fact, it may be impossible for researchers to control for all these variables, without sticking subjects in a controlled lab environment! Unfortunately, this is highly unlikely to work for long-term studies, such as the weeks and months needed to test chronic coffee consumption.
Instead, individuals can test their own coffee reactions. They would need to control or tag variables in their HRV tracking app, to provide context, while modifying their coffee consumption. This isn’t different from how individuals use HRV to understand and optimize their training and recovery “doses”.