your right about the converer. It is not the one specifically for your car. If it has air tubes on it, then what the dealer likely did, was go to the local auto parts store and buy a universal catalytic converter. The tubes that you mention are for air injection, mostly used on older cars that needed to have a little fresh air added to the cat to help clean up the emissions.
I think the reason for plugging the tubes was to make that cat work for the car, even though it is not the right one. The welding in weird spots on the piping was the technician that performed the recall making or hacking the replacement cat into place.
Now I understand this might be a costly repair, but an experienced welder at a muffler shop will be able to cut the rusted pipes off and install and weld on new ones to the existing cat.
But if you still have the paperwork from when the recall work was done and you have pictures to proove the hack job you might and I emphisize might be able to get the dealer that performed the recall to do something for you.