If you have done the rest all in butt welds you are pretty well versed in them and should be able to continue and use a butt weld here. It sounds like you are doing a kick but restoration and it sounds like the car deserves more of the same.
You do NOT just plug weld along the flange seam, You still need to completely weld the seam or you WILL have "ghost" lines once you are all done with body and paint. A quality flange tool like I bought at Eastwood years ago (made from real American made ViceGrips) does a hell of a job with little distortion.
Personally I say forget the pneumatic flanger, as well as the pneumatic hole punch, i have preached here enough why I dislike them. But hand tools are almost always better, with very few exceptions, than pneumatic tools.
If you keep your welds small and ALLOW THEM TO COOL NATURALLY you can keep warpage down to a very small amount or not at all. If you cool them with air or water or something you WILL have warpage.