A: I understand where your concern is. With this item, there is a lip around the edge of the skylight that eliminates the gap you are asking about. Once installed and properly shingled, that gap will be eliminated.
A: There is a a lip coming off the edges of the skylight that once installed will fit correctly in the 9"x 9" hole you're creating. Flash would not be needed once properly installed and shingled.
A: The skylight is just a venting skylight. We have many customer who order it to get more ventilation to their shed.
A: This product is only designed for Handy Home Product Sheds.