I don't use silicon on anything. Once you put it on nothing else will stick to it. I use a polyurethane caulk. There are several brands on the market. I use one called Quad. It's available in several colors from many of the big box stores. I e-mailed the manufacturer and was told it would be excellent for what I wanted it for. It has held up well. I generally tape off both sides of where I want to put it. That way I can get a nice straight line. No reason to do anything to the roof if it doesn't need it. Check for shrinking also.
B.O.