I have no clue what one would use on a silicone boot because I have not and will never install one. For the 2 tiny spots on the metal flashing I use through the roof. The storm collar I use siliconeYes, but they all use boots too. Also, I have most of the system installed. The only part left is to cut the hole in the roof, drop the chimney pipe in, screw down the fire stop, install the flashing and storm collar. If I wasn't afraid of heights it would have been done already.
Are you talking about the boot to pipe seal, or are you talking about the seal between the flashing and roof metal?