robbie, watch the video from the beginning of this thread to have a better understanding what the procedure involves.
It looks like the recall kit they get is just a pump motor with a filter attached to it, the filter is just a small teabag-like looking piece of mesh attached to the bottom of the pump, also some new washers and wire harness.
they remove your old plastic fuel pump assembly from the fuel tank and need to disassemble it to remove the old pump from it. they then insert new pump with filter into the plastic assembly, change some washers and seals, route the new harness and insert the whole lot back into the tank.
you gave them the whole pump assembly, hence made their work much easier, all they had to do was remove your old plastic pump assembly and insert the new one, that's it, no faffing around with disassembling the old assembly.
there should not be any extra charge for it as it actually saved them time and parts!
there are however correct, the plastic housing/assembly/bracket is not replaced as part of the recall but this doesn't need to be replaced unless is cracked or broken.
the plastic housing/bracket is not a filter, it's just a housing for the pump, fuel level float and some pipes and wires.
bearing in mind they had the audacity to charge you extra for saving them time and money, I would actually double check that the part you bought from cox motors actually sits in your fuel tank...