I think you've got the right of it here. I've worked in JIT logistics as a truck driver, as a freight broker, and as a dispatcher. I've bumped docks at ports, factories, warehouses, and retail stores all along the supply chain for industries ranging from auto manufacturing to food.
When the process runs, it runs super smooth and it's a great system. But it's fragile. A tractor trailer breakdown between factories can shut the whole thing down for hours at a time, which is a pretty big loss. All of the compounded failures and shortcomings along the chain that you mention mean that we're going to be seeing the effects of this for a while to come.