The difference you're seeing is not due to holdback - that is included in the invoice and rebated later. It's due to other fees that vary such as dealer association advertising fees, etc. These are fees the dealer must pay so it's fair that they are included in the dealer's actual invoice. If this link works you can see a sample invoice showing the advertising assessment and fuel charge which won't be in the edmunds, kbb, etc. invoice figures.
https://www.fordpartner.com/partnerweb/pdf/...lan_invoice.pdf