When using Flux, you interact with two separate Kustomization types.

• kustomization.kustomize.config.k8s.io: Used by kustomize, which is now built in to kubectl apply -k .... I’ll call these Kustomize overlays.
• kustomization.kustomize.toolkit.fluxcd.io: Native to Flux. I’ll call these Flux kustomizations.

See also the Flux FAQ: Are there two Kustomization types? and the subsequent How do I use them together?.

imho this was a fucking terrible design decision by the Flux team, and it makes talking about kustomizations really difficult.