Butyl will streatch and will not run under very hot conditions. It is more expensive, lets say $3.50 a tube compared to tar caulk which is about $.99.
Butyl comes in colors also, but very limited. Black and bronze I believe.
When you caulk, take some either mineral spirits or alcohol up with you to clean up and mistakes on the metal part. On the roof, if its comp, just don't get it on that.
Another thing, most skylights leak on the up side of the flashing. The water runs down the roof and colides with the flashing and some times spills over the flashing and up into the molded flashing to protect from leaking. Be sure and caulk very well up under this lip.
If this becomes a problem in the future, as for a small cricket to be built.