At a lower level of description, of course, what goes on in a cell doesn't resemble an assembly line, automated or not. In particular, the parts that a cell produces, protein molecules, are not picked off the production machine and carefully conveyed to meet the next part in the process. Instead they float loose to bump randomly into other parts until they meet one they click together with, in a process called self-assembly.
In a nanomachine, as in a human-sized factory, parts are never set loose to drift around. They are moved by robotic arms, shuttles, or conveyor belts from spot to predetermined spot and are assembled by mechanical force. This has two big advantages: things more much faster, going directly to the spot where they're need rather than having to do a walkabout; and parts can be designed for their function alone, instead of having to be designed for their function and also to pop together by themselves. Designing for self-assembly is a major constraint: not only must the parts that are supposed to fit together do so, but parts that aren't intended to go together had better not fit. In a regular factory, if tab A would fit into slot C, where it doesn't belong, as well as a slot B, where it does, it's not aa problem; you simply don't put it into slot C.
The nanomachine is a lot faster and simpler in some ways than the machinery of the cell. On the other hand, it has a big disadvantage: it can't evolve. Cells work the way they do in part because it's easy to make small changes that leave the whole thing working. Suppose you want to add a part to an existing machine. All you need to do is start producing it. If you get the shape right, to match the existing machine, the part will bump into the machine, latch on, and start working. In an assembly line context, you need to design not only the new part, but the conveyance equipment, the assembly machinery, the process flow, and the control mechanism or software.
Now remember that in evolution, 999 changes our of 1000 are for the worse, and die out. If you try to build a new part and get it wrong, it simply doesn't fit and nothing much happens. But in the factory model, to have any effect at all, you have to do a whole bunch of changes at the same time and get all of the right the first time.