They probably had to disconnect the exhaust to take out the tranny. Chances are that the tranny could not clear the opening unless this was done. If so, they probably disconnected it from the catalytic converter or from the headers. I can't really go beyond that.
The way to take out the tranny is by lifting the truck on a lift, disassemble the exhaust, then tranny. Then lower the tranny to work on it. This is what I've seen done as I've had to have a few rebuilt transmissions.