Also there is a flaw in your steps--always Intercompany invoice first--then only commercial invoice.
Actually no. If you are using a direct intercompany to customer process, SAP forces you to post the commercial invoice before the internal one.
The question here is if this process is a direct shipment from 1000 with billing from 2000, or a two step process, with a transfer from 1000 -> 2000, and then a sale to the customer. Since he only has one outbound delivery and no PO, it seems to be the former.