You're right, but many times a watchmaker will just regulate the movement after the initial assembly and not perform a second assembly. The second assembly is really something quite special as it's not entirely necessary, only necessary if you want to nearly eliminate scratchmarks on plates since these plates that are prone to scratchmarks will be decorated only for the second assembly. You'll also notice that new movement architecture is going to have lots of plates and bridges (chronographs are going to start having everything covered up) so that way the movement is less visible. Manufactures will claim this is for accuracy as more plates add rigidity to the movement, but it's also because the movements are cheaper to build and easier to maintain. Bigger pieces and fewer of them generally can help reduce costs.