If bolts were missing, how did the crews pressurize the cabin? Missing fasteners mean vacant holes for air to leak from the cabin. Did the crews us manual pressurization to override the auto pressurization? Were there maintenance complaints made to the mechanics and instead of grounding the aircraft for major air leaks the mechanics just signed off the aircraft as repaired and returned it to service? That is done for minor issues but if you cannot pressurize the cabin that is very dangerous as was proven when a major fuselage door blows out. If that would have happened at 39000 feet altitude many people would have gone out into the slipstream;
The door plug is primarily held in place by 12 stop pads mounted to the fuselage and 12 stop fittings mounted to the door plug. When the door plug is installed it is slid up, over and down with stop fittings behind the stop pads. The 4 missing bolts just prevent the door from moving in a vertical direction.
Here is the preliminary NTSB report that should answer your questions.
https://www.ntsb.gov/investigations/Documents/DCA24MA063%20Preliminary%20report.pdf