From the various fiberglass projects I have done on my boat and the experience Thataway documented on his fiberglass repairs, I would not assume the factory followed proper procedures for installing any hatch or thru-hull. It takes a lot of time to properly bed a thru-hull as explained in many forums here and factory does not want to and I am inclined to say, from my experience, the factory does not follow the procedures to protect cored hulls.
With that said, I like water intakes through thru-hulls. When properly located, you can use the system while underway. The location of the bait pump intake the factory installed on my boat was too high. It only works when the boat is fully stopped. Once we got underway, the thru-hull was out of the water and the bait pump starved for water. It didn't take long for the bait to die. This is one of several examples where I scratched my head wondering why a boat manufacturer missed this.
As Chuck S said, thru-hulls are not an issue, when properly installed. There are multi-million dollar boats with multiple thru-hulls. Once you install one properly, you will never again hesitate to do so.
George