I am not sure if allowing users to override default by editing/adding to a completely empty file is a good solution either. It's rather error prone and easy to, for example, accidentally type field name incorrectly.
You can make your program complain that the field is unknown too.
Personally I copy paste everything and type few things anyway, but a way to handle this is to provide an example config file with everything commented out from which you can start. I quite like this way of doing things.