Yeah, Gamestop did things in a weird way. They cancelled and shipped orders and then charged back the original payment method for $299.99 (instead of $310+tax, so it is cheaper). Everything should work out in the long run (ie. still get two XBOXs for the price of 1), but it's annoying if people want to return an order that doesn't exist/was cancelled.
Not sure how chargebacks would work. With paypal at least the seller has an opportunity to respond. You can show proof you were charged for a cancelled order, but Gamestop can provide a tracking number as well. Not sure who PayPal would try with. I'd probably rather not deal with it and be perma-banned from GS online.
All said and done, it's a total Gamestop way to do things. If they were going to cancel the order, just do it and don't ship anything out/charge anything. If you are going to honor the 2 for 1, just let the original payment go through, don't cancel and re-charge.