The MQD promotion from bookings through 10/31 and the current promotion on stays and rental cars are not for just prepaid only. As a reminder, you cannot prepay car rentals on the car rental site through Delta.
I did the MQD promotion about a year ago when Delta was first testing this out and had a pay-at-hotel stay. The MQDs posted about 5 weeks after the stay without contacting Delta.
I called Delta on Friday to confirm whether the bookings needed to be prepaid and spoke to a very competent agent. She connected with the Skymiles team and she confirmed that as long as the booking was made through the Delta Stays/Car Rental website and my Skymiles number was attached to the reservation, the MQDs will be credited to my account, regardless of prepay or pay at hotel/counter. It just seems to take a bit longer for for pay at hotel/counter to post than prepaid.
I will call Expedia later to put a note on my reservations not to deduct mileage. Thank you all for your assistance.