I spent 15 years of my career working in contract manufacturing, building and managing engineering teams building manufacturing & quality systems. A lot of what our company did was for regulated industries (defense & medical). What's not surprising at all is that Boeing customers would have conducted independent audits of the materiel being delivered to them, either while the planes were on the line, or post-delivery. That's to be expected, as is periodic external audits by regulatory bodies. What's mildly more interesting, but still not surprising, is that Spirit was so consistently upset with finished product quality that they contracted with Boeing to have Spirit employees colo'd at Boeing shops to inspect and warranty repair their planes. This is also not remarkable in electronics contract manufacturing: very frequently there are OEM employee squads staffing QA & Repair/RMA benches at contract manufacturer factories, for two reasons. 1) The OEM knows their product better than the manufacturer, and 2) Risk. Ultimately the OEM is accountable for quality to the consumer, no matter who the constructor is.
It mildly more interesting to learn that Spirit was not granted access to Boeing's MES, which leads me to believe that Boeing's stance toward Spirit is more like "they're our customer and they insist on on-site inspection & repair so we'll begrudingly allow it" than "they're our customer and we have a shared interest in quality manufacturing so we'll partner with them to ensure that happens." This is a failure of leadership and extremely short-sighted, and is virtually guaranteed to result in the sort of process failures and outcomes the throwaway describes.
It's not uncommon for OEMs to take over contract manufacturer's sites, either because of a strategic decision to conduct manufacturing operations internally [again], or due to persist or pernicious quality issues arising from specific partners' operations or at specific plants. This is relatively feasible in the case of most electronics and smaller mechanical devices, and contract manufacturers operate in a state of existential fear most of the time, knowing their destiny is in the hands of a small handful of OEM customers (just look at the impact Apple's quarterly reports and projections have on partners like Foxconn, Jabil and Pegatron). It's not practical -- or even really possible due to capital expense -- to do this in aerospace. For that reason primarily, I see no alternative than for Boeing (and others) to be forced into 100% process compliance by presence of permanent external audit teams based in corporate offices and every manufacturing & assembly location. I wouldn't be surprised, too, if Boeing were forced (for political rather than anything to do with quality) to onshore more of their supply chain[1]).
[1] https://www.sciencedirect.com/science/article/pii/S235197892...