Why didn't you order the chip variant that had the thermal pad at the top? It is possible the original design was just for that but the parts with the thermal pad at the top were not available, so the manufacturer used one with the pad at the bottom. A quick check would tell you if that pad is ground or not.
As for replacing the chip, I would have tried a pre-heater and hot air at a low airflow to remove the chip, but your Exacto knife is a good technique but does not work too well if the copper has mask over the area underneath, although you could scrape it off and then try thermal transfer.
As for the pin registration, it is the house painter's dilemma - is near enough good enough, or do we risk making it worse by trying to make it perfect?
My fracturing technique worked OK for the LM3886's on the speakers I just worked on because the pads were quite large and at one side of the module and it was easy to stress the pins' weak spot and the junction of the package.
Winner, winner, chicken dinner - a great feeling when one has debugged a problem and got it working!