Update: I've tried a few things to cut down on the wind noise and have found a solution.
My thinking is that the noise is coming from the one lateral cross member right in the middle of the thing. It's not the box because I've test driven it without the box and the wind noise is still there. So, to smooth out the turbulent flow I mocked up a laminar flow inducing co-planar platen. Or in other words, I duct taped a big sheet of cardboard to the top of the roof rack. Actually, it only covered about 10 inches aft of the cross member.
At freeway speeds, it seemed to make a difference so I went back to the garage and duct taped more cardboard to the front of the cross member. Back to the freeway. On the on ramp at 50 mph, it seemed quieter yet. Then 55 mph, then 6...fooomp! I hear the cardboard rip off. Dang it, that was a good piece of cardboard too.
About a month went by and I was too lazy to work on it anymore, until yesterday. Yesterday, I thought about it and because of more laziness I decided I didn't want to attach aluminum sheet to the rack because that would mean I'd have to remove the roof rack so I can gain access to the bottom for drilling and tapping. Instead, I went with the fairing idea.
That was a lot easier since I only had to drill and cut a few things. Here it is, works like a charm. I can hear a little buffeting up there, but much better than before. Plus, I think it completes the look of the rack, something was missing before.