There are many, but it's mainly a matter of choice. Here are some benefits:

• Docker config are immutable, where environment variable are not (this one may be both a benefit and drawback though)
• Docker config are easily manageable with docker config commands where environment variables are not
• Environment variables may collide in your container: you may use environment variable MONGODB_HOST=mongodb://foo:bar@my-mongo:27017 pointing to Mongo database but a library you are using in your application will also use this variable but expect a simple hostname such as my-mongo and throw an exception at runtime
• Config file may have restricted read permission (i.e. only the applicative user may read it), where environment variable may leak to a sub-process or anyone accessing your container
• Config file may be splitted in several parts for readability or management in your container, environment variables cannot
• When checking what are your effective container configuration (i.e. running a shell in your container and looking around), using config file is much easier than showing a bunch of potentially unrelated environment variables (cat myconfig VS. env)
• In summary, config file are more partitioned and manageable than environment variables

You may take a look at this post which is not Docker specific but may give some insights.