Sorry for the late reply. I think the issue here is Minikube. I have tried this recipe on a real Kubernetes cluster (GKE in this case) and Fleet Server and APM Server Agent successfully enrolled and show up in the Kibana UI without further intervention from the user. We also test these recipes on daily bases on the most common Kubernetes distributions and we did not have any failures with this one recently.
As to why the recipe does not work on Minikube I don't have a good answer right now (maybe just timeouts due to restricted nature of this environment). Minikube is a development and learning tool for Kubernetes and not intended for anything complex or anything that comes close to productive setups. I would recommend evaluating it on a real Kubernetes cluster.