Those are good approaches, and I wouldn't try to use manually set env vars for most things. I do tend to think they work very well for debug an dry run options though, because those are generally ephemeral, and things you might want to set ad-hoc in different environments easily without changing the config for everything in that environment, or passing around a special config which may not be updated when the real one is.

That said, I'm not married to it, if I saw something that seemed obviously better, I would switch. I also suspect that different languages may make one approach easier/better than others based on their capabilities, idioms, etc. In many scripting languages, accessing an environment variable is extremely easy. In some compiled or more strictly typed languages, the access and conversion to the expected type might be cumbersome enough to do on site that it's worse, and if you are standardizing in come parsing routine, that might tip the benefits in favor of some global context that is used instead.