Hello,
Sadly you have a big problem. I had the same and posted extensive work arround here.( I don't see it any longer) I am inteligent too and understant very well the nature of the problem.
1. All this is absolutely not related to your intervention.
2. The bolts that look scratched are from rust free alloy and they don't hold the paint well. It seems to be scratches from tools, but it is not.
3. The nuts are not stripped. Tjhose are bishings spinning in the holes of the roof metal. The access from insife the car is limited even if you droped the seeling. Some of the nuts are under the roof reinforcing braces. This is not going to help.
4. I my oppinion the best way to fix that is the following:
- The plastic supports for the roof rack components shold be CUT very carefuly and removed.When the mounting bolts are exposed they can be removed when holding the spinning heds of the bushings with wisegrips. There are many small procedure details here, but I have no time to write them down now. Let me know if interested. I have pictures too. Any way the problem is fixable.
- Talk to the dealer service that you will care for the roof itself, but they have to supply new roof rack components under warranty. In my case the dealer sent me to body shop and they cut the plastics UNDR MY SUPERVISION. Then they gave me the new roof parts and I installed them with the agreement that they will be not covered under warranty in the future.

Now my problem is fixed and I like this car very much. Again there are many fine details that if you don't follow you can permanently damage the roof. For now Don't try to undo any bolts anymore, because it will never work.

Regards

Larry