This is for my own understanding. It might be wrong but reflects my current understanding.

Helm is a package manager and templater. It stores whatever info it has about the configuration in the "Secrets" of the cluster, so it know what the current configuration is. For example, if you need to roll back, it can do look up the details of the last successful release and roll back to it.

Helm, among other things, is a wrapper for kubectl apply but if you use kubectl apply directly, then you don't get the benefit of helm storying the configuration in the cluster.