I have the wing off my limited right now as I'm painting it, so I can't give it a test. I do recall a slight "rattle" more like a vibration when closing the hatch. Certainly nothing like "a bag of bolts" and never any sound when driving in the up or down position. In the down position there is a notch in the levers which raise/lower the wing; Perhaps that is not engaged? Just a guess. I believe the only way to fix that would be to try an adjustment of the gearing at the motors limit switches.

Addendum: I went out to my shop and took a look at the wing motor and gearing. There is no adjustment to those limit switches. The switches themselves are locked into position by small pins to the frame of the motor assembly, and the large gear which the arm of the switches contact on it's rotation is an one piece plastic with no adjustment. Even if you remove the motor with its small pinion gear and slip a notch on the larger gear it will make no difference as the timing of the on/off is strictly related to the lobes on the large gear and its contact with the arms of the limit switches.
The shafts that power the wing up and down are rectangular where they insert into the large gear. Thus they can be placed into the gear only in one of two ways; Each being 180 degrees from the other. That way you can insert the roll pin at the outer end of the shaft no matter how the shaft is inserted into the gear. IF THE LARGE GEAR is worn and thus no longer truly rectangular, then the shaft may not turn in it's full mode of rotation. That may be the only thing that could prevent the wing from fully closing, unless the pivot pins are worn badly at the levers which attach to the wing itself.

One other thing to look at are the rubber bumpers that are attached to the levers which raise and lower the wing. With the wing raised and standing at the side of the car look at the top of the lever which is attached to the wing. There are two rubber bumpers, one on each side that when the wing is closed should contact the cars body. They should both be in contact with the body in the stored/lowered position, keeping the wing from rattling when closed. They won't do anything when in the raised position. Might want to check that.