Lets me start by saying I love this game even without the listening to the remarks that will follow. 
Working in the field of supplying Automatic guided vehicles, both to transport parts to the line and cars on the line, I have a few remarks:
Usually the Axel and motor assembly is a separate line that at some point is “married” to chassis in the marriage station or line. I say line because most assembly of the cars is done in continuously moving lines by people. When robots are doing the work it customary the work is done in a stationary station. As the stations in this game use robots the game is accurate.
So to my knowledge the flow of production is (commonly):
Main line:
- chassis assembly: on floor conveyor at fixed positions with welding robots.
- Paint: usually by dipping whole car in a primer or paint bath in continuous motion, But spray painting like in game is done too.
- First stage general assembly: Continuously moving floor conveyor, inside car parts.
- Second stage general assembly: A continuously moving overhead conveyor in which cars hangs, for work on underside of car.
- Marriage: Chassis hanging in overhead conveyor is married (bolted together) with axle & motor assembly which comes from a separate floor conveyor line. Mostly done in a continuously moving motion.
- Third stage general assembly: A continuously moving overhead conveyor in which cars hangs, for more work on underside of car and mounting of wheels.
- Final stage of assembly: Continuously moving floor conveyor, the finishing touches.
- Quality control: Usually at fixed positions (like in game). The word rework is usually not used as this would imply bad quality
Between these parts there are usually longer stretches of either floor conveyors or overhead conveyors that function as buffers so that when one section has a breakdown the other still can continue (at least for some time).
Axle&motor assembly line:
- Continuously moving floor conveyor where axles and motor assembly is put together, motor placement can be a stationary position (usually then the start of the line). At the end this assembly is married to the chassis.
Motor line:
- Usually motors are build in a separate factory on a continuously moving floor conveyor. but final fitting of some external parts (connection of hoses/brackets) is done in the car assembly factory in a continuously moving overhead conveyor which feeds the motor to the axle&motor assembly line.
Door line:
- Usually doors are removed after in first assembly stage after paint and assembled on a separate continuously moving floor conveyor after which they are placed back in the final assembly stage of the main line.
The element from above which is missing in current game are the overhead conveyors which contrary to floor conveyors need be in closed loop (the construction in which the cars hangs needs to return to start of line after the car is removed from it at the end), and the continuously moving lines. Although as work in the game seems to be done mostly by robots I’m not really missing that part.
Overhead conveyors for cars could be tricky in combination with the current overhead resource conveyors. Which bring me to another part which is that the resources are usually not supplied that way but manually pulled carts and/or AGV’s (Automatic Guide Vehicles), that drive on the factory floor. Putting the parts ready for distribution by those manual carts and/or AGV’s can be a whole separate line(s).
Last suggestion is being able to use AGV’s to replace the floor conveyors as this makes easier for delivery paths of resources (when done over the floor) to cross the production line.
Reading over this post I realize the isometric nature of this game would make manually driven carts and AGV’s look clunky when cornering. Also a continuously moving conveyor line might be hard to do to justify the effort, and since there are factories that operate that way the start stop stations used in the game are perfectly fine.