I think I know what you're talking about with the Down East rod holders and multiple rods on the side rails.  There's a way you can spin the Down East outside board rod holder around so that it then sits to the outside of the rail and a couple inches higher.

It would be better to have some kind of extension that puts it up about 6 inches though. 

Edit/correction: I was just looking at my boat and reversing the rod holder does not add 2" in height,  it just offsets it 2" to the outside of the rail (4"" total). It's still very effective because the outside board rod now sticks out further than the inside board rod if they are the same length. Plus, the reels are offset so even with the down easts being crowded on the rail like mine (4 per side rail), you can still easily crank in the reels without removing them from the holders.