Take another Atlas on the lot for a drive for comparison - if it's normal, it will do it. My transmission shifts smoothly and quietly, almost imperceptibly. Maybe try another dealer. They may be happy to handle a warranty issue, as they get paid by the factory.
Transmission issues happen - statistically, there has to be a few bad of the thousands that are made. We had a bad manual transmission in a Mercedes we bought new one time. It would pop out of first when you went to take off. Factory replaced it.