If you remove the lower stainless (below the glass) you'll find the reason for the problem. Mopar engineered a gutter under the stainless (where the rubber gasket sits). This gutter holds water, worst of all it acts like a greenhouse. Since the sun can't shine under the stainless the water can stay under there for many, many days/weeks. It's even worse once you get little twigs/dirt and leaves under the stainless. The dirt, leaves and twigs soak up the water and keeps the gutter wet continuously. The vinyl (I believe) gets glued down into the gutter then covered by the stainless. Once water gets into the gutter it wicks its' way under the vinyl. If you remove the stainless you'll see. If you re-glue the upper part of the vinyl it should help but it won't keep the water from getting into the gutter (very poor design). When I owned a 67 Barracuda fastback in the 70s it had bad rust under the lower stainless and it leaked into the trunk. Three years ago I bought a 69 Barracuda fastback with no rust anywhere. I knew what was going to happen because I live in a very humid climate with lots of rain. The first thing I did was remove the back glass, remove all the pins that hold the stainless and put three coats of brush on undercoat in the gutter. Then I replaced the glass and had the glass man seal the whole gutter with urethane and nice rubber strips. I was willing to own my car without any stainless just to keep it from rusting away.
I drive my car all the time so it sees some bad weather but it shouldn't ever rust around the back glass.
PS - The same thing happens in the front cowl (fresh air duct). Twigs, dirt and leaves get in there also. The stuff gets wet and creates a sludge that stays wet (greenhouse effect). That's why so many owners have to repair the cowl area as well.
treblig
