No, I am talking specifically about comments or documents that explain the "why" behind parameter choices. For canonical defaults that are shipped with an app, this should be documented in a user guide and in the appropriate parts of the source code, not inside the config file (which most users would never care to read, and which would be worse to read for most developers who might care or change it).

For local config files that are not shipped with the package, they should still be source controlled in a separate repo (yes, even if you personally are the only one using it, like your local Postgres configuration or something), and you should use a good practice to 'deploy' any changes to your config from the repo into the actual location where the application can recognize that config -- meaning that documentation about the "why" of the parameters once again should absolutely not be embedded inside the config file itself.