Channel customers are managed by Partners. The Amortized Cost at Partner level will match the Azure Portal, but the Amortized Cost at channel customer level is lower than Azure portal.
The reason for the discrepancy can be due to costs for subscriptions with place holder 00000000-0000-0000-0000-000000000000. Those costs will show at partner level but they cannot get assigned to customer via Partner Generated Billing. This is an expected behavior.