We're looking at making it easier for people to bring-your-own-helm-chart[1] and have GitLab deploy it. There's value in keeping the chart in the project repo, and there's value in decoupling the chart and putting in a different repo. I'm fascinated to see which becomes best practice.
I can't say I'm thrilled to put deployment-specific values in the repo. Maybe the solution is to keep the chart itself, with its defaults, in the repo, and then have a configmap or third-party resource in Kubernetes that contains the values. To deploy anything, you use the Kubernetes API to find the app's values and merge them into the template.
I wouldn't be surprised if one day Kubernetes might support that kind of templating. I also wonder what kind of system Google uses internally. They have been rather silent about offering good advice here.