Yes, Encrypting config file is common. DPAPI way uses symmetric key and therefore, if someone gets the key, he can decrypt.
In my case I used an RSA asymmetric key. That way encryption with public key is performed. Decryption can be performed only with private key protected and held by server in SQL database. On application side, users and application don't need the decrypted secret but need to stay encrypted. Simply, public key is to encrypt and private key is to decrypt. And nobody can easily get the private key.
Furthermore, when it comes to cloud platform like Microsoft Azure, we have to use certificate way which is of also RSA.
My case took almost 1 month to understand the complexity. I completed this task just recently.
The decryption is performed automatically by indicating the thumbprint of private key in the config file.