I'm not sure how the Limited fender flares are supposed to look. The best advice I can give you is to keep the area of the door clean and waxed often to prevent rust.
As for that hole, you mean the one in the frame in the 2nd pic? That is a crossmember of the frame. You will see that hole on the other side. It is a tube.
What is that tube for? I don't know it's purpose. Is it safe to just hose it down with water at the car wash?
Like I said, it's a crossmember to the structure of the vehicle.