I'm not sure how the auto manufacturers do it, but I've worked at companies that did it both ways.
One was a military vehicle manufacturer, where each part was modeled at the coordinate system, them mated to the proper placement at the assy level.
Aircraft manufacturers I have worked at do it the other way. The parts are modeled in space at their position in the finished aircraft (except of course fasteners and related hardware). The parts were still properly mated, but even without the mating, they would appear in the correct location.
The logic seems simple. If the part is going to be used in multiple assembles, each at a different location, then model at the coordinate system. If the parts are unique and used only at one location on one vehicle, then model relative the vehicle absolute coordinates.