I would just seal the inside of the rebate with whatever you're using as a finish. As far as I'm aware, bedding internal glass or mirrors is only to stop rattling. So unless your mirror is going to be moved constantly, I reckon you don't need any bedding.
The acids in silicon can also attack the silvering on the back of the mirror so another reason not to use it. If you have not got the mirror yet get it "foil backed" as this not only protects the silvering from moisture it also keeps all the bits together if it gets smashed.