You can ref other rnamespaces

clusters/kairos/apps/fluxrepo.yaml

@@ -2,7 +2,6 @@ apiVersion: kustomize.toolkit.fluxcd.io/v1
 kind: Kustomization
 metadata:
   name: flux-apps
-  namespace: flux-system
 spec:
   interval: 10m0s
   path: ./apps
@@ -11,3 +10,4 @@ spec:
   sourceRef:
     kind: GitRepository
     name: flux-system
+    namespace: flux-system

clusters/kairos/apps/kustomization.yaml

@@ -1,5 +1,6 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
+namespace: apps
 resources:
 - namespace.yaml
 - fluxrepo.yaml