Ask HN: How do you manage 12 Factor Environment Variables?

As the last paragraph of https://12factor.net/config states:

"In a twelve-factor app, env vars are granular controls, each fully orthogonal to other env vars. They are never grouped together as “environments”, but instead are independently managed for each deploy. This is a model that scales up smoothly as the app naturally expands into more deploys over its lifetime."

How do you do that practically while avoiding bundling vars in files? I know you can use e.g. docker secrets for credentials, but what about bare metal? For example, how would you manage deployments of a NodeJS service? Or a create-react-app project?