I have pulled a few windows and haven't seen sealant between the glass and the rubber but I have seen sealant between the rubber and the car body. I can't say for sure if that was done from the factory or by a professional auto glass installer or just a PO trying to fix a leak. Did you buy your window gaskets yet? If so and they were from OGTS or another reputable supplier then I would call them and ask for their professional opinion. These windows are not sealed in place like new cars are. You might as well do the carpet last because why track dirt and what not into the car while installing the dash and the window, especially if you use some type of sealant. How would you feel messing up your new carpeting?