Engine Cover

Removed engine cover to cure rusting problem on base plate of hinge.Having removed the base plate, I separated the upper metal section from the base by removing the two allen bolts. They appear to have some silicone sealer on the threads, presumably to secure them in place once they are screwed home.Is this anyone else’s experience? Do I need to squirt some silicone back on to ensure they stay in place?
Also, the bolts protruding vertically from the car that secure the base plate are a bit rusty but I can seen no way of replacing them. Any ideas, please?