But the fee is per transaction not per item. So adding this to the item price wouldn’t be correct either.
If you purchase 1 file, then that file is Item Price + $2 Handling Fee = Total
If you purchase 2 files, then that is Item Price A + Item Price B + $2 Handling Fee = Total.
You cannot add it per item, because some customers may purchase multiple items, and then that value would be incorrect. It’s not 2 / item, it's 2 / transaction! 
Plus, the handling fee is clearly added there in the checkout box, it’s in your screenshot just above the total price.
