I know on my TR6, the factory used two types of caulk. Around the rear side lights, they used Dum-Dum as they did on the floor to frame bolts. It was still off white and soft. No rust where it was applied. Along the wing to body seams they used a hard caulk. The areas where this was applied dried out and broke a long time ago. Once that happened, water was allowed to come into contact with the primed surface. A lot of rust all along the wing seam.
Restorers do tend to prepare the metal much better then the factory, and the restored cars tend not to see, or sit out in the weather, as they did when first bought. These cars do not see the miles they did when first sold. Over time, dirt accumulation and body flexing will cause scratches and cracks that will eventually rust. The question is, will the rust that forms on these pamper cars rear it's ugly head in two years, five years, or the 10-15 years it took to show on the original? I doubt it.
That said, I will be using the 3M strip product previously mentioned to seal out the water and provide a tighter bond for the joint.
Oh, on undercoating, if the bottom of the wing's lip is sealed with undercoating and the joint is not sealed, water and dirt will collect and eventually rust.