There should be line discounts on project item transactions and project invoice in order to invoice items with use of projects item transactions. You often invoice item transactions which originate from project item journals and project purchase orders instead of using a project sales order.
You have trade agreements with discounts, and use for example both retail/sales orders and projects to deliver/invoice items to the customers. But since discounts are not fully supported in project module, then you need extra manual work to support both scenarios.
As-is there are discount fields on some project business documents, but you need discount fully implemented on all documents in order do fully support discounts in same way as using standard sales order, including transfer from project quotation to project. For example there are now no discount on item requirement, WBS, project invoice report, project adjustment etc.
There are also different behaviour when discount is used as-is, either the net amount is reduced with discount or the unit sales price is reduced with discount on the project item transactions. It should be consistent with net amount reduced with discount, with discount field in addition as on sales order. I have submitted this to Microsoft and it has been postponed - LCS link: https://fix.lcs.dynamics.com/Issue/NotFixed/1187145?bugId=3838627&qc=80d1139efec6e5968deca0fc4bae275f16a19c67ad29f3682eafb8d8f3ceeec2