question

The atomic order APIs can only calculate the order total etc. for you based on the data that is available at the time the request is made. In this case you are using the atomic order endpoint to create the order, and then you are adding the discount after order creation in a separate call (/v3/merchants/mid/orders/orderId/discounts). If you perform any adjustments to the order after it has been created you are responsible for properly updating the total to account for those adjustments. If you want to continue to do this then you need to properly update the total after you add the order discount. However, I would suggest that you pass the discount in the atomic order request instead of making a subsequent call to add the discount. Also, you should be testing in sandbox, not production.