Prepayment with Tax for SO

We would like to process credit card payment via standard JDE functionality from Sales module.

However, the standard process suggests running settlement R0042002 after shipment confirmation but before invoice printing. Clearly, the goal is to print the invoice as pre-paid or customer receipts. I am concerned about the taxation part. The tax comes into picture during the sales order update.

I know we can go for delayed capture process however business wants to include taxes on the prepayment. Is there any suggestion to achieve the business requirement ?

We did thought about marking up the payment as well but it varies and some customers are tax exempt.