The primer pump injects fuel directly onto the intake valves. Opening the throttle just dumps it into the carb, where it still has plenty of opportunity to condense anywhere along the intake runners. In very cold weather, the primer is far more effective and also reduces the chances of lighting your air filter on fire during start.
I believe the primer lines connect to the same fitting that the manifold pressure line is attached to, which is why it doesn't prime all 6 cylinders.