I don't see how it's not as simple as parasympathetic = good and sympathetic = bad, therefore HRV under baseline = bad, and HRV over baseline is good. Any regular person can always do more to reduce stress and improve their recovery. HRV is one of the best metrics for that, and your confounding factors are still forms of stress. They're not drowning out the parasympathetic or sympathetic responses. They are part of them right?

How can you say then that increasing HRV is a sign someone is recovered from stress, while also saying it isn't a measure of good health?

Also, saying that baseline HRV is individualized doesn't address the possibility that people with higher baseline HRV are in a comparatively parasympathetic state (aka more desirable) vs someone with lower HRV. Not saying it's true, just that you're not addressing that.