BBBowtie, I have seen dropping the glass into the body, it is an old trick. I don't like it at all, just seems hokey to me.
mallard, I am not sure I understand you, there is no room below the quarter windows. Not unless you go below the body line (seam)and that wouldn't be chopping, it would be sectioning. You couldn't change the door windows, you would be below the bodyline.
You can chop one and leave the center rear window stock, it is done all the time and was done on the Rod and Custom dream truck in 1954.
I just re-read what you wrote. You are talking about going below the body line but only at the quarter glass while still lowering the top. I thinkif that line was disurbed it wouldn't look very good. Just make the windows out of plexiglass, mine lasted for 20 years till I sold the cab. They still looked pretty good.
I think I have decided to not use them at all when I finish my chop (been sitting for a few years, while I work on other projects).