2016 Hyundai Santa Fe - Roars and knocks

when the rear passenger window is down… there is a deafening noise and the vehicle vibrates at highway speeds… there is also a knock from under the vehicle (rear) at lower speeds

Did you just acquire this vehicle ? The wind noise from having just the rear windows down has been around for a long time . Usually putting the front windows down also can reduce it .
As for the knock have a shop look at it because it could be serious .