No one is chiming in, so I will make a stab at it,
First I would take it back to the shop and keep bugging them until they make it right.
It would be hard to diagnose without being at the rig to look over every gasket and mating surface. I am sure you have already checked to make sure they have all the gaskets back on and they are pliable.
Also, check at the window to make sure it is closing correctly and all the way up. My kids just bought a 10 XLT this past Xmas up in Tacoma. I noticed it had hardware foam insulation above the passenger door. I thought, what the heck. And it was a whistler when hitting highway speeds. So further research showed window not closing all the way, looked good but glass short or not hitting all the way up. I replaced the window regulator and noise went away.
One of the tricks of old was to shut a piece of paper in the door and pull the paper. Check for resistance. We would do this in the area of concern and 3-4 other places around the door. Normally doors are adjustable and can be made to fit tight and still keep a nice reveal. The body shop who done the work can certainly do any adjustments.
Stay after the shop, that noise is certainly a distraction
Gary