EU Vat Tax , First Party with Multiple Registrations

 Our Main Legal Entity located in EU country A has additional VAT registrations in country Y and Z but we only have one ledger set and one OU. When a PO is raised to be invoiced to our Z registration we use the Ship To for the physical flow and the Bill To Z to identify the Tax Regime , the Bill To location country being set to Z . As a result when the invoice is matched to the PO the correct regime is picked up.
However when we want to enter a invoice without PO we only have the Ship To available on line level so impossible to indicate to which Regime this invoice-line belongs as Ship To Country is not per definition equal to the Bill To country and we want to capture the Ship To country for Intrastat reporting purposes ( by the way it is not possible to enter the Ship From either !! )