The design of the manufacturing lines and the resulting supply chain are not independent of each other -- you can trace features from one to the other -- but you cannot take apart the supply chain and analyze the designs of its constituent manufacturing lines and actually predict the behavior of the larger system.
AFAIK there's not a great definition of a complex system, just a set of traits that tend to indicate you're looking at one. Non-linearity, feedbacks, lack of predictability, resistance to analysis (the "you can't take it apart to reason about the whole" characteristic mentioned above"). All of these traits are also kind of the same things... they tend to come bundled with one another.
(And no, this is not "my" definition, it's how it's defined in the systems-related disciplines.)
The set of system designs that exhibit naturally stable behavior doesn't overlap much with the set of system designs that deliver maximum performance and efficiency. The capability gap between the two can be large but most people choose easy/simple.
There is an enormous amount of low-hanging opportunity here but most people, including engineers, struggle with systems thinking.