If you use third-party Helm charts, you eventually need to add onto the generated objects in a way which the chart doesn't support, and then you're up a creek without a paddle. This is precisely the use case which Kustomize tries to fix and it was the only real strength which Helm had to begin with (i.e. the ease of installing third-party software on your cluster).

In the meantime, because you must install Helm into every namespace in your cluster into which you desire to install charts, it's a massive resource hog and security risk. Charts themselves also need to be hosted somewhere, so you end up needing to install Chartmuseum, Harbor, or Artifactory (if you didn't have Artifactory already), and they have their own operational costs.