I worked in auto glass for 10 years.
My 20 cents-
If you are using laminate glass its easier to glue them in, less chance of breaking it driving the track on using setting tape. But once its set, its set, no moving it so make sure its in the right spot. Clean the track real good and use urethane in 3 spots about 3in long beads, ends and middle, do not use silicone. You will have to drill the glass out of the track in those spots if you ever have to replace it though.
If your using tempered glass, drive the track on with setting tape. As long as your glass is clean and prep'd, the correct setting tape thickness is used and your track is clean and in good shape, it wont come off.
Your local auto glass shop would probably drive your tracks on for you cheap (There is a proper tool BTW).
Your regular home improvement clear silicone sealer shouldn't be used anywhere on a vehicle IMO. It corrodes steel when it cures and retains moisture, guaranteed rust. Ive seen way to many vehicles damaged because that crap was used.
Okay I'm done