I know almost nothing about welding, but I had an experienced body man helping me with my body work. He used what I think you refered to as plug welds, and did an excellent job with a MIG welder. When he finished I don't think it would be possible for you to tell where the welds are.

I don't know if this is a common practice or not, but with panels that were hard to get clamps on, he used self taping metal screws to hold the panels where he wanted them, then removed them after the welding was done. I think he did an outstanding job. I couldn't be more pleased with it. Allen