Discounts are working on standard priced items. However we are using Tier and Flat Tier priced items and found out discount are not working for both types using the trade agreement and that is halting us from going live. We double check with Microsoft and they acknowledge that it is not working.
Idea behind how it should work with the trade agreements.
We have to setup line discount(sales) in the trade agreement with either an amount or a percentage. We would generate the invoice from the billing schedule (Sales order to invoice) this result in the invoice having correctly reflect the discount amount. The problem is there is no indication of discount on billing schedule lines/ details or header in the subscription billing module.
After updating the above logic just need to check all the reports/ inquiries these are reflecting the discount applied on the billing schedules/ line or billing schedule line details.