With limited gunwale space you should use vertical trees for board rods. This way you can put 2, 3, or 4 rods vertically in the same space that 1 rod holder takes up. For multiply dipsys you want the rods lined up horizontally.. You could mount a track in that space. Your tree mount will mount to the track and so will your dipsy cradles.

I would NEVER use a system that runs the rods across the transom wall. How would set lines off the back of the boat? You would have to reach over and around etc to net a fish. The back of the boat needs to be open to let lines out and bring fish in. Look at the way a charter boat is set up. Rod holders down the side walls and the transom area open to work lines and bring in fish.