Re-sealing the rubrail

I know I've made a post before about having to much water come out when the drain plug is pulled. I thought it was caused by backwash..which some of it is. But I seemed to have found another culprit. It seems that the rubrail is leaking a bit. I have a stratos and the rear end sits real low in the water. It only seems to be an issue when i'm loading and unloading the boat. I guess I'll have to start keeping an eye on that. I have two questions.
1. Can you just use regular silicone to seal it up?

2. Should I be worried about water in the transom?

Thanks
Jesse