Hello,
maybe there's a way to just not show Fedex methods as an option if someone chooses to send in stock items now and backorder items later?
You can use a
return true; after checking if you have these type of products in your cart or directly enable the "price per product" option through your shipping method configuration page and then go to your "in stock items now"/"backorder" products configuration page, and block that shipping method through the "shipping prices" tab.
Also note that when you set the "group package" option of your shipping method configuration page, you'll have one product per package, so the problem is globally coming from what the FedEx platform return.