No, DO NOT use silicone! While it does seal, it doesn't have strong adhesive properties to stick to the glass & frame. And if you try to re-glue the hatch later, without COMPLETELY removing all of the silcone, you'll have a difficult time with bonding.
If you just want to squirt something in there to fill the gap, use the same type of
urethane windshield adhesive that's used to bond glass to metal. Something like this
Transtar Autobody - Urethane Windshield Adhesive . Or any of the 3M Windo-Weld type of
urethane windshield adhesives will work. No
silicone.