Do the rattles persist when you drive with the top up but with all 4 windows a little down (2-3cm)? If that's the case just clean the upper ''rail'' where the windows shut with a m-f towel wrapping a credit card or similar and then lube it with WD40.
I too had roof rattles, left it over at the dealership 4-5 times but with no permanent fix.
I now consider it a part to maintain, whenever various rattles pop up -once every 2-3 months - I gradually open the roof and practically lube everything with a sponge wet in WD40, every joint, plastic and elastic bit and seal that I see in front of me and additionally the seals on the doors, trunk and hood.
Hope this works for you too, guys.