My guess of what may have happened reading between the lines is - Boeing originally possibly instructed Spirit to loosely fit the plug and not secure it because

My guess of what may have happened reading between the lines is - Boeing originally possibly instructed Spirit to loosely fit the plug and not secure it because they planned to remove it to fit out the interiors. In this case Boeing would be accountable to secure the plug door after the interior is done to the right specs Somewhere down the line, Boeing possibly decided not to remove the plug and instead just load interiors through the bigger openings only. They possibly either did not document this change and think through implications and instructions changes for Spirit to secure the door plug instead or did so but Spirit possibly missed. So the bunch of planes may have been delivered with loose plugs that Alaska and United found. All the implications of outsourcing without sufficient supervision and hand-offs made in the parent point would have a bad effect. The question FAA is probably asking is if Boeing or Spirit has deviated from documented production practice in this area, have they deviated in other areas.