databases are entirely different, those would be the database.js files yes. Out of curiosity, that database config structure looks like something from Alex the Entreprenerd - YouTube. While it works, it’s not what we recommend.
Regarding that auth.secret, that has nothing to do with the database. It’s the secret key used to encrypt the JWTs.
If you are referring to the env() functions, I would suggest reading this documentation which explains how they work: Configurations - Strapi Developer Documentation
Outside of that, I’m not sure what you are asking.