Techniques have changed, but the one thread that remains is that it is built where access is easy for the workers. You don't see too many ships built in the middle of the ocean. Likewise, doing a scratch build from in zero G vacuum environment would be very difficult and probably take considerably more time and effort than one that has its hull sections built on earth and then is assembled in space. A space build would require a lot of EVAs and while times may change, human endurance doesn't.
Access for workers would be trivial for a civilization with transporters.
The same goes for a "scratch build from in zero G vacuum environment." Using the energy (E) from the same power source that makes warp drive possible, the transporter could beam into existence all the mass (m) needed for the entire ship in a single pass (E=mc^2) making sure that every detail of the ship was perfect, or at least was exactly how it was designed down to the quantum level (a la Heisenberg compencators).
With the above method no EVAs by humans would be required.