In your particular case, in the most ideal scenario, all the required namespaces should already be created before running the kustomize command. However, I know that you would like to create namespaces dynamically as needed.

Using a Bash script as some kind of wrapper can definitely help with this approach, but I'm not sure if you want to use this.

Below, I'll show you how this can work, and you can choose if it's right for you.

First, I created a kustomize-wrapper script that requires two arguments: 1. The name of the Namespace you want to use. 2. Path to the directory containing the kustomization.yaml file.

kustomize-wrapper.sh

$ cat kustomize-wrapper.sh
#!/bin/bash

if [ -z "$1" ] || [ -z "$2" ]; then
    echo "Pass required arguments !"
    echo "Usage: $0 NAMESPACE KUSTOMIZE_PATH"
    exit 1
else
    NAMESPACE=$1
    KUSTOMIZE_PATH=$2
fi

echo "Creating namespace"
sed -i "s/name:.*/name: ${NAMESPACE}/" namespace.yaml
kubectl apply -f namespace.yaml

echo "Setting namespace: ${NAMESPACE} in the kustomization.yaml file"
sed -i "s/namespace:.*/namespace: ${NAMESPACE}/" base/kustomization.yaml

echo "Deploying resources in the ${NAMESPACE}"
kustomize build ${KUSTOMIZE_PATH} | kubectl apply -f -

As you can see, this script creates a namespace using the namespace.yaml file as the template. It then sets the same namespace in the base/kustomization.yaml file and finally runs the kustomize command with the path you provided as the second argument.

namespace.yaml

$ cat namespace.yaml
apiVersion: v1
kind: Namespace
metadata:
  name:

base/kustomization.yaml

$ cat base/kustomization.yaml
apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization

namespace:

resources:
- deployment.yaml

Directory structure

$ tree
.
├── base
│   ├── deployment.yaml
│   └── kustomization.yaml
├── kustomize-wrapper.sh
├── namespace.yaml
└── overlays
    └── prod
        ├── deployment-a1
        │   ├── kustomization.yaml
        │   └── patch.yaml
        ├── deployment-a2
        │   ├── kustomization.yaml
        │   └── patch.yaml
        └── kustomization.yaml
    
    
    

We can check if it works as expected.

Creating the namespace-a Namespace along with app-deployment-a1 and app-deployment-a2 Deployments:

$ ./kustomize-wrapper.sh namespace-a overlays/prod
Creating namespace
namespace/namespace-a created
Setting namespace: namespace-a in the kustomization.yaml file
deployment.apps/app-deployment-a1 created
deployment.apps/app-deployment-a2 created

Creating only the namespace-a Namespace and app-deployment-a1 Deployment:

$ ./kustomize-wrapper.sh namespace-a overlays/prod/deployment-a1
Creating namespace
namespace/namespace-a created
Setting namespace: namespace-a in the kustomization.yaml file
deployment.apps/app-deployment-a1 created