Caulking for transom glass
I wouldn't use caulk. It's going to be difficult to get everything in place without inadvertent squeeze out and other minor catastrophes. Get some glazing tape or simply some double-sided high density foam tape in the appropriate size. Ideally it would be slightly narrower than your stops and set to the outside so that you don't see it once the glass is installed.

Run that down your stops, press the glass in place, and you're good to go. I would consider putting it on both sides of a glass actually. This will  reduce the chance of vibration noise even more and also reduce the chance that you'll crack your glass when installing your stops.