Interesting thread.
I've been thinking about this for my 8" soft bait rods in my FC465. It has rod holders on the sides below the gunnels (hard cell foam ones that the rods clip into using velcro straps). Fine for setting out in the morning, but a hassle when you've started fishing and just moving to another spot, starting a drift again etc.
And I don't want to have a rocket launcher across the stern bait station etc, or place rods in the rod holders built into the gunnels (reels exposed to spray at times, rods bounce around).
So the concept i came up with sounds similar to FishMan's. It was to have a couple of lined rod holders mounted on the upper side of a flat piece of wood that's attached via a bracket to the metal pole the passenger swivel seat sits on - about 30cm from the deck.
The design in my head is that the rod holders/flat wood are on a hinge and can move from the horizontal to the vertical plane. Horizontal facing the stern when underway and rods stowed, vertical at rest or when not in use.
With fly rods, you could have them in a carved cradle, lined with foam and maybe some velcro straps over the top to stop them moving.
I know people with centre consoles who have rod holders mounted vertically behind the bow, either side of the dry storage area. Reels below the spray level, rods pointing to the sky. Seems to work, but obviously an issue if you want to cast from that area - rods in the way.