kubectl apply -f ~/git/infra/secretproject/prod.{json,yaml}
One JSON/YAML file too uwieldy? Generate it using jsonnet/CUE/dhall/your favourite programming language. Or just talk directly to the Kubernetes API. You don't have to use Helm - in fact, you probably shouldn't be using Helm (as the whole idea of text templating YAML is... thoroughly ignorant in understanding what Kubernetes actually is).
> Layer a service mesh with custom overlay networking that abstract upon k8s clusterip.
You don't have to, and you probably don't need to. I'm happily running bare metal k8s production without anything more than Calico, Metallb and nginx-ingress-controller. That effectively gives me 'standard Kubernetes networking' ie. working Services and Ingresses which is plenty enough. And if you're using a cluster deployed by a cloud provider, you don't have to worry about any of this, all the hard decisions are made and the components are deployed and working.