Cars were not painted with glass installed. It makes no sense in painting procedure. They would have to mask the windows. Overspray on parts from poor masking is common during repaints. Many just papered off the windows and did not worry about overspray that the felts will hide when installed. Some don't even take the felts off. Big diifference in restoration painting and collision repairs.
I think it's obvious that the glass would not be installed, as that would have required additional tasks to clean up, but the small amount of paint that went thru the inner panel holes would not affect the 'back side' of the inner mechanisms. it's too bad we don't have access to the Fisher body procedures used (for any year) as I doubt they changed this sort of thing over the years.
My question had to do with the guides, channels, door latch, etc. There was paint on my door latch, and some on the back (interior) side of the guides/tracks (corresponding to the holes in the interior of the door, making it seem that the internals were installed prior to paint, so when the door inner side got painted (lightly), some of the paint went thru the holes to the internal parts. There was NO overspray on the glass or the parts attached to the glass.