First of all, as far as I'm concerned, it was stupid of Triumph to go to the screw on stanchions. The dzus fastener type that slides on is a much better arrangement. That said, my original body had the dzus type, but the body was so bad, that I got a post 60k at a fire sale price (literally, but that's another story). I had to get a whole mess of stuff to use that body, and of course, the screw on stanchions was one of them.
After I assembled the whole windscreen, I went to put it on the car, and thought the same thing you are thinking now. The big problem I ran into was the the fit of the stanchions to the body wasn't close with the windscreen fully assembled. I had to loosen the stanchion to windscreen screws, start the big screws into the body and work back and forth until everything was snugged down. By this time, I had forgot about putting in some gasket material that I had decided to use between the stanchions and the body. Too late now, I don't ever want to have to remove this again. :hammer:
However, if I did do it over, I would put those gaskets in. I doubt there was anything in there originally, as by this time, Triumph really didn't think you should be removing the windscreen on a regular basis. After all, they did eliminate the aero screen attachments and a lot of other neat stuff because of costs.
OK, rant over...

I'd put some gasket material in there.
Edit: One more thing. If you are using new stanchion mounting screws (the big ones) from one of the after market suppliers, check the fit into the recesses before you go to mount things up. I found that the heads were just a tad too tight, and may need some fitting.