Rust around rubber seal

So I have all the carpeting and trim out of the rear of my truck and am preparing to put down some CLD (Vibration Damper) and noise barrier. In the prep process I found these rubber seals on the passenger side wheel well surrounded by rust.

My questions are what purpose do they serve? Is there a good way to seal the holes after repairing the rust? What would be the best way to approach the rust repair?

I have very little experience with metal work or repair but would rather get this fixed before it get sealed in by the CLD. Most of my experience is with wood and fiberglass for audio fabrication.

 

[92Explorer4.0]

to me it dont look like its all the way rusted thru. if its not i would would grind off the surface rust and prime it and lay ur CLD down. just my 02 cents tho. James.