I don't know that this is the best way, but I use a module that instantiates a proxy object. It populates the config object behind the proxy at startup and crashes with a useful message if a value is missing. If something tries to get an undefined value at runtime, the proxy also throws an error. This way the module documents the config, and the app crashes if something is missing rather than silently trying to run with an undefined value. You can also use object.freeze or what have you to make the config object immutable for most practical purposes.
I don't know if that's the best way either, but it's the model all the most successful engineering cultures I've been part of have used, which certainly says a lot for it in my view at least.