I would think that it was put there to make assembly in the factory easier. When the engine/transmission/suspension cradle was raised into the engine compartment, the down pipe must have been part of that assembly. With the rest of the exhaust mounted to the body, the flange would have been the meeting point between the body and the cradle.
It also would make removal of the cradle much easier assuming the flange can be separated after some years without destroying it.