I haven't had a problem with rust or paint bubbling at all. You know, if you get the pieces to fit right, solder follows heat and will fill up even wide gaps automatically. However, those pieces have to fit correctly no matter if you're welding or soldering or brazing. Just a different way to skin the cat. I worked as a commercial welder in the late 60s, by the way. Quick way for a young man to become an old man in the miserably hot weather we get in Dallas.
You can also usually put the flange backwards...that is to say flange the old metal (the part you're saving) and let the patch panel fit forward into that flange area. If you're concerned with drainage, let common sense prevail and do it that way. In that case the flange will be a rear overlap to the patch panel and any water coming from above will run right over your joint. I've done it that way plenty of times, but generally I like to flange the patch panel since you can move it around easier.
Another thing I do is to buy some water-based black satin X-O Rust paint and coat the back side of any part that I can. If it is a door, I'll tape up the drain holes and pour about 1/4 of a beer can in there. Tilt it all directions, letting that paint cover everything. Be certain to let it run into the seams well. I use that paint because it dries fast but it remains flexible so it doesn't crack down the road. It sort of reminds me of liquid caulking compound. And I've mentioned this here before, but I've also used J-B Weld. Especially the Kwik-Weld stuff they make now. You can mix it up, apply to both the flange and the panel, join them and hold in place with some high quality masking tape. It will set up in about 5 minutes and cure in about 5 hours. Then you'll have it done without using any heat at all. I repaired my truck where the roof cap joined the pillar on the passenger side in 1978 and you still can't tell anything was ever done.
