Your idea might work but would require manual manipulating the spreadsheet.

I've solved a simular problem before with a custom solution. In that case is was to automate invoicing a very large number of small shipments in OE. A view displayed all orders that were shipped and could be invoiced using various ranges. All within the range were selected by default but the user could then deselect (by clearing the tick box) those not to be invoiced at this time.

Maybe something simular could be done for your PO issue and also asking for the freight to allocate. Each individual PO would get received with it's proporation of the freight. You would still end up with the many invoices in AP to be replaced with one.