Replacing the transmission is always fairly complex, particularly for a home mechanic. But if a shop has a lift I don't think it would be too bad to pull just the transmission from the bottom of the car.
The torque converter is seperate from the transmission. There is a splined shaft that sticks out of the transmission. The torque converter slides onto that shaft and then has four studs on the opposite side that get bolted to the flywheel. So if they ordered a transmission the converter would be a seperate part.