The invoice number being automatic should not make any difference. Once the invoice is created, the automatic checkbox becomes unchecked and the assigned reference remains as if you had entered it manually.
Can you illustrate what you refer to with screen shots?
I thought were referring to the receipt reference. I suspect the reason invoice numbers don’t show when receivable invoices are automatic is that there could be many. Further, if other receipts are edited or credit notes are issued, the allocation could change, rendering old receipts incorrect.