Clarify ways for modifying config.toml when using GitLab-manager Runner

doc/user/clusters/applications.md

@@ -127,7 +127,11 @@ before deploying one.
 The [`runner/gitlab-runner`](https://gitlab.com/gitlab-org/charts/gitlab-runner)
 chart is used to install this application, using
 [a preconfigured `values.yaml`](https://gitlab.com/gitlab-org/charts/gitlab-runner/-/blob/master/values.yaml)
-file. Customizing the installation by modifying this file is not supported.
+file. Customizing the installation by modifying this file is not supported. This
+also means you cannot modify `config.toml` file for this Runner. If you want to
+have that possibility and still deploy Runner in Kubernetes, consider using the
+[Cluster management project](management_project.md) or installing Runner manually
+via [GitLab Runner Helm Chart](https://docs.gitlab.com/runner/install/kubernetes.html).
 
 ### Ingress