So I’m in agreement with you that this is not standard practice. However, if a vendor is giving you a discount (at all) it is a good thing. Therefore, I recommend that you remove the discount terms (or override the discount amount) when you pay the bill.
Assuming that you are using QuickBooks desktop, go to the pay bills window and select the bill. By putting a checkmark next to it. At the bottom of the screen you should see a button that says discount. It will be located to the right of Go to Bill. Click on that button and enter the correct discount amount.
Thanks so much for reading!