Handling unavoidable rust (probably?) contamination in arc welds
I am not an expert welder by any means but if you were to watch enough YouTube videos on the subject you would come to know that welding very thin materials is an art unto itself. You said nothing in your question about the type of welder that you use (ARC, MIG or TIG) but one of these types is probably going to be much better at avoiding melt through on thin materials.
From what I have learned it takes lots of practice to establish the expertise to be able to successfully weld thin materials. The 3/32&quot; that you quote should be weldable without pin hole melt through with the proper skills.
I believe that if you can avoid getting the heat so high to avoid melt through that the rust on the inside should not be a problem.