Both the boost pumps and ovrd/jett pumps are designed to provide vapour free fuel to the engines. The air is returned to the tank and the fuel goes to the engine. The outlets of the pumps which all connect to the engine feed manifold are have check valves which must be forced open by the fuel. When the center tank pumps are supplying fuel, the main tank outlet check valves are held closed by the higher output of the ctr tank pumps. This prevents any fuel from flowing through the main tank pumps. When the center tank pumps have emptied their tank, the main tanks are now pushing their check valves open and forcing the center tank check valves closed thus preventing any fuel from feeding back to through those pumps.
If none of the pumps are working, the fuel bypass check valves are pulled open by the suction effect from the engine driven pump and will allow fuel to pass to the engine.
The crew would actually have a warning message alerting them to turn the center pumps off when the tank has emptied and I doubt that they would ignore that.
Possibly the only thing that could have happened is that the aircraft attitude became so extreme at the low speed that the aircraft was flying that all 4 of the main tank pumps and the 2 bypass valves pickups became uncovered and fuel flow to the engines was interrupted.