Do not use silicone.
Use a self leveling sealant on the roof. You can use Dicor or another brand made for rv roofs. Check to be sure it is compatible with a fiberglass roof. Use non-leveling on vertical surfaces.
If you use silicone, nothing, not even silicone, will stick to itself when it needs to be resealed or touched up.
If it's just to seal the edge of the gutter and will not be in contact with the roof, you can use LEXEL. It's crystal clear. I've used it around my taillights and windows. It's a little harder than silicone to work with, just follow the directions. I used painter's tape to help get clean lines (just don't leave the tape on while it dries).