Kustomize is a Kubernetes native configuration management tool that allows customizing application configurations without templating. It takes over existing application manifests and is built into the kubectl command. Kustomize introduces an overlay pattern to customize resources through a kustomization file. Other configuration tools like Helm have template languages that can be ugly due to templating and conflict with other tools, while Kpt automates editing but requires functions for transformations. Kustomize aims to provide a simpler way to customize configurations and can integrate with tools like ArgoCD. Challenges include dealing with incompatible upstream changes and difficulties reviewing pull requests.