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Can a MAF sensor from a 2003 MN6 be swapped out for a 2000 MN6?
Yes, and no. It can be done but you will need an adapter harness to go from the 3 pin 2000 MAF connector to the 5 pin socket on the 2003 MAF. The 2003 MAF has the IAT sensor mounted in the housing which is what the extra 2 wires are for. Then you will have to reacalibrate the MAF airflow table in the computer. If this step isn't performed your car will not run right, and you may even throw some codes.
I swapped a 2002 MAF into my 99 without tuning the table and it ran ok for a while. I only needed to get it home, about 2 miles, and once there I reflashed the table. This was a stock motor at the time with an LS6 intake, headers, and exhaust, so the bolt-ons may have played a factor in it running better than if the car was bone stock.
If you don't plan on recal'ing the computer you will be better off keeping your stock MAF.