Sorry for responding so late - I really appreciate all the comments.
The good news is the car really was garage kept - the rear window seal is as good as new. The rust appears only to be contact rust where the screw went in, so the overtightening theory sounds right on target.
My immidiate solution is to simply just stop the rust. I.e. I will remove the chrome rain rail and spray some rust arrester in the area. This should buy some time for me to take it in and have the rest done. The spots are not in an open place, and even if you were staring at them you'd still have to look for them to find them.
Moedip - the "new metal" stuff is exactly what I am trying to avoid. Otherwise an update - she is in the shop right now being readied for another huge trip to New England next weekend - I am having the cooling system flushed, coolant swapped (yup - somebody put green stuff in it
) , the b2 piston replaced along with a tranny flush, belts replaced, and oil changed. Then she is going for ride from Washington, D.C. to Cape Cod!