This is a question for the guys in the Paint and Body Shop...
My answer would be to butt weld as flange welding makes it hard to work out any warpage (can't hammer/dolly the weld you just made to stretch the metal back out) and it will trap future moisture causing the rust to come back.
Mike B
In addition to Mike's comments, using a flanged seam leaves your panel with the possibility of a ghost line in the paint finish that will show EXACTLY where the seam is. One layer of sheet metal will expand and contract more quickly than two layers. Given enough heat (think truck/car show in the sunshine) and enough cycles of heating and cooling (expanding and contracting), the panel will show a ghost line. This won't happen overnight, but will take a year or so. But rest assured, it can and will happen. This video shows a repair done on the bottom of a wagon's tailgate where a flange seam was used. The entire car had been restored by the owner, who did a beautiful job. The only flaw I could see was where the flange repair resulted in a ghost line.... watch the video.....
