And that is the smoking gun I was waiting for.

All the ingredients for an ineffective Quality Assurance are there.

A)Selecting the most junior engineers as certification authorities

B) Emphasis on testing and defect discovering as non-value adds (the article quotes at least one manager referring to it as "polishing an apple")

C) Active suppression of legitimate defect reporters (engineers let go or otherwise ostracized for legitimate defect reporting)

D) Undermining of labor's ability to act as a check valve to management taking the company into dangerous waters (South Carolina plant)

E) Engineering around regulations instead of just building the plane that needed to be built and accepting the cost. (No simulator time became a non-negotiable marching order due to the emphasis on cost cutting)

F) Misaligned incentives and strategy after the McDonnell Douglas merger (Forget the box [plane], people already assume it's high quality. Focus on the financial/value engineering in order to maximize shareholder value.)

F is especially damning, since part of that financial value engineering was heavy reliance on outsourcing, which if you don't combine with a strong Quality first in-house QA team to manage the acceptance criteria, leads to debacles like the supposed to be standard, but not AoA disagree warning. This is a corporate behavior pattern that must absolutely be avoided in life/safety critical systems.
At the end of the day, the laws of physics give not two shits over what shareholder value you've created, or how many people's lives it will cost. It is only the will of your engineers to proof the plane against catastrophe that will result in a product that won't come back to haunt you later. It's okay to keep up some pressure on cost; but at the end of the day, safety and Quality must win. The system must be modelable from just what is in your engineer's head, backed up by your spec docs, in a reasonable amount of time.

I'd like to know more about how point D played into this mess as well. In all these stories, I'm not seeing much information on what the union was actually doing to try to improve the situation.

I know there were walkouts, but most of the reporting focused on those being focused on wages, work conditions, etc. Typical important union stuff. However, that "stuff" is like the cosmic microwave background of labor relations. It seems like quality/safety concerns should have been a bright point on somebody's map of stuff to run down. If not, why?

Were people raising safety/quality issues with Union reps?

Were those concerns effectively received and recommunicated by union reps? Or just translated or left to fall by the side in the interests of the typical union agenda items?

If Union reps accurately represented concerns which were reported to management, did management understand the message? Or did they oversimplify the problem to "let's avoid the unions"? Who made that decision?

If not, where did the breakdown in communication occur? What caused the breakdown?

There's a fairly complex social web of influence at play in workplaces, doubly so with Unions, and I think this is a serious enough case that everyone involved should have at least some investigation done on them, if only to illuminate a new corner case in how not to handle concerns with safety critical work.

As Demmings would say "A system is perfectly tuned to yield the results it produces." What else about Boeing, and it's employee relations made it manufacture such a lethal breakdown in communication?

By no means is this "apple polishing". No amount of polish puts a glimmer on 300+ corpses.