Holes in the roof must be kept to a minimum. Most areas like this leak on the leading edge of the area that catches the rush of water down the roof that hits the skylight area. Its like a ship's bow cutting the water, some will erupt up and go up and over the flashing and then leak.
Sometimes a good crikett must be built to stop this. Mention cricket to your roofer. Then good strong caulking will aid, but will need touching up each year. I like a good Butyl Rubber caulk. It will stand up to heat and cold and will expand and contract, BUT it will only last a couple of years.
One piece of advice, go up on the roof with the roofer and watch what he/she does and then you do that periodically.
Remember, when you have someone out to do the work, you will never know if it worked until the next heavy rain. So make sure there is a guarantee in writing so you are covered.