Rear window question

I just got my 1978 Ford Granada back from the auto body shop. I had all the rust problems repaired. There were many holes under the rear window
on the pinchweld. My question is if the rear window seal has to be glued to the pinchweld. There was a rubber-like materiall that I had to remove before removing the window. Is this material used to prevent water from sitting on the bottom pinchweld or is it used to prevent water from getting under the seal and into the passenger compartment? Finally, should I use urethane or a silicone material to seal the window?
Thank you
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