Sometimes the decision is based on what resource you will have access to changes in production. Depending on the size and complexity of your organization, receiving changes made to the production configuration file may require several levels of management approval and hours (if not days) of delays. Although modifying the prod database (albeit a custom-made application) can be relatively simple.
This special database application can also be useful so that users (or admin users) can modify the data.
Another consideration is whether you want to restart the application when data changes. Sometimes changing the configuration file may cause a restart - it depends on the web server, etc. If you want to be able to change on the fly, without restarting the application, the database is the place to store data.
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