If you originally chose to pay fees out of your Federal refund, and they have been paid due to a delay in processing at the IRS, then once the IRS releases your Federal refund, it will still go to an intermediary bank through SBTPG before it goes to your own bank account (or card.) It is the temporary bank account at SBTPG that the IRS has on file for the refund payment. SBTPG will receive it and send it on to you.
You will not have to pay the product fees again. Have you already paid the 39.99 service fee for that payment method (44.99 for California filers)? If so, you won't have to pay that fee again either.
It will still go though SBBT but they won't take the fees out again. Maybe the extra $40 Pay with Refund fee if they didn't take that when they charged you.
Expand What if the IRS reduces your refund, then after step 3......
"The same sequence of events occurs if the IRS is still holding your refund 36 days after your original estimated refund date, except that we'll also debit the Pay With My Refund fee (if any) in Step 3."