HMMMMM I have a 74 challenger that i bought WITHOUT a rear window anf front windshield. It also had a rusted out trunk floor and rusted spots in the trunk fill strip down to the trunk lid. So, obviously the window that was in there was leaking...and for a long time.
Now, that being said, I simply repaired all of the rust and made sure that the entire channel for the rear glass fit the glass with no large gaps and that the front windshield channel was in great shape.
Then I had the entire car painted.
Then i bought a used rear window and took it to a auto glass shop for installation (also had them obtain and install the front windshield as new ones are readily available for reasonable prices). My cost for this was $100 + $20 shipping for the used rear window, and $275 to the auto glass show for the front windshield and professional urethane installation of both. So just under $400.
I have no leaks!!! Have checked many times when washing the car, and when caught in a flash rainstorm at a local car show. I would believe that today's urethane sealers, and trained installers are so much better than what was used back in the early 70's in the factory that it isn't even funny. Remember into the late 60's they still were using gaskets for the front and rear windows, so, the urethane sealers were of early design but in the early 70's. Also, i don't believe that they gave the installers at the factory enough time to do the job properly.
Incidentally, the front windshield the auto glass shop supplied, turned out to be a "little thinner" than the original OEM glass. So to get it to properly come up to the level of the roof and surrounding area, they had to put in a "bridge". I.e first they put in a layer of urethane and let the car sit in their shop overnight to "set up". Then they put fresh urethane and the glass in. They said this is very common on the older classic cars. It now fits perfectly and no leaks!!
In other words have it properly prepped and installed with good urethane and activators on the glass, and there shouldn't be any issues..
Just my two cents worth!!