Condensation will form on the inside bottom of the top roof panel. Not being air tight may increase that. I don't know why you have rust only there. Only to say that it sounds like your truck did not rust from snow, rain, salt or drip rail problems or leaks from the outside. Just rusted from condensation on the "inside". Water accumulated and it did stand and rust. Cold outside metal and the heater going on the inside....or hot outside and air conditioning on inside..just a guess. I am sure not an expert on condensation. I suppose the windshield rubber could leak. Rain/snow did blow up under the brow.
Does not really matter, the fix will last another 50 years.

Right is right, even if everyone is against it, and wrong is wrong, even if everyone is for it. - William Penn