If a customer inquires about why there is no merchant shipping amount on their order, you should first check the order IDs in SP under Finances>ListFinancialEvents to see if the shipping was included.
If it's not there and they paid through Amazon I believe they would need to wait for the settlement report to see it show up in the sales transaction.
If you see the shipping included but we are not showing it in Stratify, then create a JIRA.