When editing an application you can enable/disable databases on the Connections tab, and when editing a database connection you can enable/disable applications on the Applications tab. As far as can tell these are separate settings. What’s the difference between setting each of them?
Enabling and Application on for a Database Connection vs Enabling a Database Connection for an Application
In my opinion, it is totally the same to allow which user database can be accessed by which Application.
However, a small note is that on the Application configuration, you will be able to delegate permissions to specify what the application can do on the database.
If you use the API then you will see this clearly. API does not interact directly with the data, it goes through Application, so you can design Application A to read only data, Application B can modify data.
Hope this helps.