> My holy grail will still be landing on a good multi-layer configuration setup for Rust CLIs. Ideally CLI flags merged over top of environment variables merged over top of configuration files.

I did that for Python if you are interested: https://github.com/kdeldycke/click-extra

You create your CLI with Click as usual, then Click Extra introspects your "--parameters" to build up support for a corresponding configuration file in either TOML, YAML, JSON, INI or XML.