In a properly functioning quality and safety management system, there's no awkward in-the-middle. The "open door plug" procedure is a planned part of the construction, inspection and maintenance of the airplane. And even if there was a doubt, the thing to do in that case is stop and document the doubt, and then document the process of discussion of the doubt, and then document the decision, including whatever change to the quality system may be needed to avoid this doubt arising the next time.

The problem here is not that Boeing does not know how to run both the original quality system and the system to modify it if necessary. The problem is the quality culture that puts "implementing the quality system" above "make line go up" is degraded.