If you Pay with Points the full value of the ticket will be charged to your card. At the end of the booking process you will have the option to redeem points to offset the charge at the rate of 100 points per dollar (40,000 points in your example).

I doubt that American Express will "match" the statement credit to the airline transaction, and you should still receive the 2 points per dollar bonus (800 points in your example) on the airline transaction. However, I do not have a Premier Rewards Gold Card to test.