Um, I'm the guy - and the joinery is already 'gone' even though I took it out in one piece I will not be reusing it.
If you are going to redo the wood anyway then your options are wide open.
The knee idea would be great and you might even be able to make it so the chain plates are completely visible inside the cabinet just like in many other boats.
I really like the way you take pictures. They really show what is going on.
Good luck with your project.
I'm sure you have good reason to replace the interior woodwork as I know you are very experienced.
Just as a warning to others though the replacement of interior joinery so it looks good and matches is often a much bigger job that it would seem at first blush.
It is one thing to do structural repairs where mostly strength is important.
It is quite another thing to do interior joinery where, fit and matching existing finish and utility are all important.
I would think that replacing the joinery on this project would probably be at least as much work and probably more work than the structural part.
But I'm a few miles away so you know best.
I was a cabinet maker in a past life and all I know it it always seems to take me a lot longer than I figured it should to do cabinet work on a boat.
If you change the orientation of the chain plates from for to aft to side to side you will have some cap rail repairs to do that will show, yes?
As you can see I'm very concerned about creating ancillary finish projects during the process of repairing a structural problem. I've been burned before.
A very classic case of this when someone replaces an engine and they have to cut into cabinetry to fit the new engine.
I've seen several of those jobs that just never looked right and it severely reduced the value of the boat.