In a new build, the areas where there are deck penetrations for the various fittings would be solid fiberglass. However, this is a labor intensive way of building a boat and most production boats do not have this.
The purpose of over drilling and filling with thickened epoxy is to protect the wood core from water intrusion. Once water gets into the core, it causes the core to rot and delaminate, which weakens the deck structure. Generally most fittings are through bolted as this is a stronger method than self-tapping screws into wood and fiberglass. In some areas screws may be the only option due to access or in some low load situations, like attaching a dodger.
While it is a little more expensive than creating your own thickened epoxy, I've been using
West System Six10 or Jamestown Distributors
Total Boat Thixo. These thickened epoxies come in a cartridge that fits into a caulking gun (Hint: If you go this way, get a heavy duty caulking gun, not the cheap $2 ones.). The big advantage is easy of use, much neater and cleaner. No mixing and filling syringes.