On BMWConfig the term used for Invoice is Wholesale. The $1000 you mention in the BMWConfig PDF specifically lists as, "Offer to Dealer Over Wholesale."
The price your dealer is giving you, assuming it is before any incentives, is exactly $1000 over invoice.
Incentives like Holiday Credit, Loyalty Cash, and the BMW Ultimate Drive app cash back should be taken off AFTER the negotiated price. In many cases that puts you well under invoice and this is completely doable and okay.