To me the issue seems to be that certain modern management approaches fail to see the value of many if not most "soft" factors: Customer satisfaction, trust, long term loyalty, employee satisfaction and motivation and such. If it can't be seen in SAP it gets ignored. You can measure and online monitor the time it takes to install every bolt and nut and how much torque got applied but the other soft elements are forgotten.
Plus Boeing had a heavy focus on legal terms and settings with "watertight" contracts, however when supplies still did not arrive on spec and time they were surprised and had to change their leaned down organisation and change processes in a hurry.
The third issue I see is that they reduced their staff, loosing experienced specialist know how in the process while sitting idle in terms of launching new programs for too long. This is why the next program will have to be expensive. New people need to learn their trade from scratch. Look at Airbus for comparison and how they fine tune the A320 over many years: Sharklets, engines, cabin, ACF door arrangements, tanks and center wing box, new flap settings. Step by step they are keeping their teams busy.