If I was going to repair seam rust, I would make a job out of it. Any
bandaid wont work. That stuff will break you heart after you spent
$$$$$$$$$$$$$$$$$$$ and time. Dont let anyone else do it for you cause they
wont give it the work and  attention it needs.

I would gouge the caulk completely, sand where I can to bare metal,and
remove the corosponding interior panel. Use POR15 marine clean and Metal
ready first. Put each in a spray gun ( seperately of course) and put the
nozzel of the gun to the seam and pull the trigger. The point being to force
the product all the way through. Besure to make a mess on the interior or
you didnt do it right :>). Repeat with POR15 metal ready and then POR 15
paint ( any color you want to use). POR15  Porpatch is POR paint with a
filler. Squeeze in a liberal amount on top of the paint and hope that rust
infiltration remains conservative. Smooth out any seam with your fingers
immediately. These products must both  be used before either drys completely
so they can stick to each other and the vehicle. Practice on some
unsuspecting car. Thats what I'd do.. May be for worse cause you cant be too
careful in this department. Good luck