We are inviting more feedback on this issue.
Current design is based around the following assumption, we'd like to know if this is wrong:
When an operator specifies a custom price for a particular lineitem, Transactor assumes that the sales person has decided to set a special one-off price for that item. As such the price is not to be further discounted or else this could lead to confusion. An analogy is a guy (bob) behind the desk at a Paint Store. His customer is a know Trade customer who gets 40% off RRP. Bob picks up a Can of Exterior Sky Blue and says 'this is our last one' but you can have it for £10. The customer nods and the item is entered onto the order as 'Blue Paint Special Price .. £10'. If when he finalises the order the 40% discount was applied, the shop would be selling this 'special' item at £6.

If on the other hand, the item is not intended as a One-Off special price, and is regularly sold at that new price say £10. Then the shop should set up code for the item giving it a Price under the 'Reduced - End of Line' price band such that the correct price will be brought onto the order, then the Trade discount will correctly apply on top of that.