We have the rear canvas setup on out 21EC and last year did not use the canvas. With the frame folded down, the two outside rear seat back cushions can be fastened to the frame, which is enough lower so they don't slide under it. The cushions install far enough further toward the centerline so that the center cushion can be dispensed with. There is the added benefit of making the seat bottom area shallower and more comfortable.
As far as modifying the stern rail, It would be fairly easy to put in several new vertical tubes from deck up to the horizontal rail, using deck fittings like the present ones and rail fittings they sell that will clamp over the existing rail at the top.
The existing setup really is a poor design. You end up with the cushions pushed under the rail and the rail pushed into your back.
If you ever get as far South as Marblehead let us know.
Larry