The best thing you can do is take pictures, document everything and get it back to your dealer. It sounds like you have some serious problems going on.
Do not paint anything on top. It could void the warrranty.
While these roofs are made for someone to walk on on, they're not made to carry cargo. So I wouldn't add any roof racks.
It would be good if you could post some pics. We could then see exactly what your talking about and it could help if anyone else is experiencing the same thing.
to the forum.