First off--I'm no expert..
But I hate the seam sealer GM used--it hardened up,the bond failed to the metal and failed to keep water out,and caused a lot of floors to rot out up here..the 3M stuff isn't much better..
I've seen glass companies use fiberglass filler like tiger hair to fix rotted windshield frames,but welding in new metal would make a better longer lasting repair in my opinion..body filler isn't flexible enough and may pull away from the seam when normal driving and heating/cooling cycles expand and contract the metal...
I once caused a windshield frame to rot out fast on a truck I had--by applying clear silicone RTV around the old crumbly rubber gasket--the stuff has acid in it--about 6 months later there was big holes where the RTV touched!..
..no doubt some water probably entered first and started the rust,but the RTV accelerated the process a great deal..
I have used butyl rubber caulking intended for metal gutter seams with good results under floor patches,but I'm unsure if it will accept paint on an external area and not have it come off ..
