I've looked into this and I came up with one idea.

├── base
│   ├── [nginx.yaml]  Deployment nginx ns: default
|   ├── [nginx2.yaml]  Deployment nginx ns: default
|   ├── [nginx3.yaml]  Deployment nginx ns: default
|   ├── [nginx4.yaml]  Deployment nginx ns: default
|   ├── [nginx5.yaml]  Deployment nginx ns: nginx
│   └── [kustomization.yaml]  Kustomization 
└── prod
    ├── [kustomization.yaml]  Kustomization 
    └── [patch.yaml] patching namespace

You need to have 2 directories, in this setup are: base and prod. In base directory you should use your base YAMLs and kustomization.yaml file. In my scenario I have 6 YAMLs: nginx/1/2/3/4.yaml based on Kubernetes Documentation, and nginx5.yaml which looks the same but with additional spec.namespace: nginx.

In base directory:

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

resources:
- nginx1.yaml
- nginx2.yaml
- nginx3.yaml
- nginx4.yaml
- nginx5.yaml

And 5 YAMLs with nginx.

In Prod directory:

You should have 2 files. kustomization.yaml and patch.yaml.

apiVersion: kustomize.config.k8s.io/v1beta1
kind: Kustomization
namespace: ns1
bases:
- ../base
patchesJson6902:
- target:
    group: apps
    version: v1
    kind: Deployment
    name: nginx-deployment-5
  path: patch.yaml

$ cat patch.yaml
- op: replace
  path: /metadata/namespace
  value: nginx

When you will use kustomize build . in prod directory, all nginx-deployment/-2/-3/-4 will be in the namespace: ns1 and nginx-deployment-5 will be in namespace: nginx.

~/prod (project)$ kustomize build .
apiVersion: apps/v1
kind: Deployment
metadata:
  name: nginx-deployment-5
  namespace: nginx
spec:
  replicas: 2
  selector:
    matchLabels:
      app: nginx
  template:
    metadata:
      labels:
        app: nginx
    spec:
      containers:
      - image: nginx:1.14.2
        name: nginx
        ports:
        - containerPort: 80
---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: nginx-deployment
  namespace: ns1
spec:
  replicas: 2
  selector:
    matchLabels:
      app: nginx
  template:
    metadata:
      labels:
        app: nginx
    spec:
      containers:
      - image: nginx:1.14.2
        name: nginx
        ports:
        - containerPort: 80
---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: nginx-deployment-2
  namespace: ns1
spec:

Useful links:

• Kustomize Builtin Plugins
• Customizong
• Kustomization Patches