Pretty simple really, to an engineer
"Even so, it's not immediately clear exactly how a permanent Earth-orbit facility would help in the process of plugging together largely prefabricated modules or components."
Depends entirely on the design. If one component has power and propulsion, it can in theory chase down the other parts, but soft docking each part in a long chain requires docking mechanisms and cameras on each to line them up. At some point it makes sense to have your assembly tools done once rather than on each part, and to leave them behind once you are done with them.
The space station itself required many EVA's to connect and deploy "largely prefabricated modules or components", and those guys needed to be somewhere in between EVA's.
The way they are packed for launch, and the way they are unpacked once they are used are different. Solar arrays and radiators are the most obvious of these.
Lastly, leaving earth orbit requires passing through the radiation belt. Electric propulsion is fuel efficient, but slow, you do not want your humans to ride along while the main spacecraft is doing it's slow climb. Your choices are a tug or booster that gets you quickly out of the radiation zone, and then heads back by aerobraking for the next trip, or the astronauts wait on the ground or in orbit until the main ship is high enough, then ride a capsule quickly out to join it.