The features you mention might be useful, but they're certainly not required.

If your program has grown so complex that users would benefit from modular configs, references, and so on, then a configuration file is the wrong approach for configuring it. You should rather provide a custom UI for users to modify the program's behavior, and persist the configuration transparently in the background for them. This can be done via a CLI, GUI, API, whatever.

The fact that tools like GitHub Actions, Ansible, Kubernetes, etc., abuse a format like YAML to make it work as a DSL, and we needed to invent tools like CUE, Dhall, and Jsonnet to manage this mess is absolute insanity. Most programs don't need such level of complexity. And for those, plain JSON, or minimal configuration formats like the one discussed here, are good enough.