I am under the impression that 3D Secure is opt-in by the merchant.

3DSecure is not opt-in in South Africa. It is mandatory for all eCommerce transactions.

If CD is not allowed in SA, is there a way to add and credit a bank account? 

To credit a bank account, we have a payout system that we can give you more info on. You can do this manually and upload a CSV file or submit a request via API, make a payment for the total amount to be transferred, and we will split it accordingly. More on this here

Some of the payment workflows our systems do cater for are not available in South Africa, for either integration or compliance reasons.  

What does DR refer to?

DR refers to a deregistration transaction. This is to delete a stored card token from our systems eg. when a customer needs to change or add new card details.