I think in most cases for rod holders, just good size screws would work fine assuming you are not fishing with huge rods/reels with heavy pull like done during shark fishing or offshore bent butt rods, etc.
For the outriggers, definitely backing plates to help distribute the load. My older Renken boat would flex the entire gunnel with the outriggers. Lots of stress on them. Never had an issue with gunnel flexing over 20+ years but they were through bolted with backing plates. The rod holders on that boat were the plastic ones with screws and I never had one fail, even with offshore Penn 113H rigs and catching dolphin, etc.
This option might keep you from having to put in more of the access ports. Only ports for outriggers but not have to for rod holders....
Also, bed all the holders down and also screw holes using 4200. Does a few things: 1. No rust creeping from underneath SS (Ask me how I know). 2. No water to get into wood. 3. Helps to add strength to mount for screws and will help screws from backing out.
One more....when boring holes out for holders, always use some epoxy to seal the exposed wood. I use the 5 minute epoxy with really good success. Water prevention is key here.