Since gate assignments aren't final until your departure day (sometimes hours before departure, YOU DON'T KNOW FOR SURE that your flight leaves from T3 and not T2.

This is a common misconception about DL's facilities at JFK. Bottom line is it's no more than 15 minutes to get from one end of T2 to the other end of T3, so definitely use the Medallion/Premium checkin at T2, regardless of your gate assignment.