Alvin, to be fair 90% of the stuff I'm working with is factory bonded glass.
Some well meaning folk may have had a go at some time trying to seal a water leak with silicone (bathroom) sealant.
There are specific products made as you mention,but I'm still not convinced,but that's just me!
If it works for you,that's fine.
In your application it's OK as you're not relying on the sealant for structural reasons.
The simple fact is most modern monocoque car bodies rely on bonded glass for structural integrity! (scary!)
The problem with silicone is it 'contaminates' the pinchweld,the very area I apply bond to.
Then the bond doesn't take,and causes failures.
I pefer to use urethane where possible as it dries to a more 'natural' rubber look,it's also a product I'm more familiar/comfortable working with.