You don't need a flange.
They have welding equipment and they have clamps and they have pipe and they have cats. You don't need to completely rebuild the front end of the exhaust just to insert a cat, but they might have to cut off the new pipe to get a new cat to fit.
The guy you went to seems to not know what he is doing. I would not go back there unless he is willing to fix his screw up for cheap, or for free. Even then, I would not trust someone who just assumes to know the best way to tune a car.