To avoid extreme weather helm in a quartering stern wind, which is the problem you are describing, I suppose you could try tinkering with the COP by making the "sail area" of the canoe profile greater in the bow than the stern. That should help to create some lee helm -- that is, to increase the bow's tendency to blow downwind (by getting the COP forward of the CLR).
Glenn describes the low stern design effect far better than my equivocating “perhaps a purposeful design element”. That is a proven design solution common to most decked canoes.
I would look at some of the existing decked canoes of similar length and dimensions; Sea Wind, Sea1, even the Poke/Phoenix Vagabond
Those decked canoe designs all have a very low stern stem. Same for the Mad River Monarch, Sawyer Loon and even the 1970’s Hyperform Optima and hardshell Klepper Kamerad. The stern stem on the Monarch is only 7 inches high, and the other designs are similar.
That low stern stem is so common on decked trippers that I have to suppose that is a purposeful design element, perhaps so that a rear or quartering wind has less exposed stern to catch.
I have paddled all of the above mentioned hulls, and currently own 4 of those models among the family decked canoe fleet. The only decked canoe we have that does not incorporate a low stem is the 1971 Old Town Sockeye. Bow and stern are both 13 inches high (it is the Winnebago of gear haulers). In a quartering wind, even with an absurd amount of gear weight, it gets blown around far more than the low stern sheer models.
With the low stern sheer the rear deck, tapered up to a 12 to 13 inch deep center, is effective in keeping following waves out of the cockpit, and the more voluminous bow provides the buoyancy needed in oncoming waves.
You argue that you don't want to keep your feet on the foot pedals for comfort reasons. Then don't. Retract the rudder unless and until you are in those uncontrollable wind or current situations that are flinging your canoe around. Surely that happens only a small minority of the time. The point is: You don't have to use the rudder if you don't want to, but it will be there as the best solution for wind problems when you need it.
Besides, if you are a sit & switch paddler, you should for efficiency always have your feet against a foot bar or foot pegs, regardless of whether you have a rudder or not. Of course, when you don't care about efficiency and just want to relax, you can take your feet off the foot bar or pegs and move your legs into a more comfortable position. Again, like a rudder, they are a tool -- available if and when you need them.
The above mentioned OT Sockeye is pretty rudder dependant in quartering winds, likely because of the tall stern. The Sockeye (AKA the Sea Wimp) is the yellow and black one below (Optima, Sockeye, Vagabond, Monarch):
https://www.google.com/search?q=deck...mP4c6wJlobFnM:
As Glenn mentions, with the rudder up I still have my feet at least lightly on the rudder control pedals most of the time, in part for oppositional paddling force to keep me in place, and in part because that leg/knee bend position is most comfortable. The MRC Monarch incorporates a pedal design feature that some folks like (I’m one) and some not; There is a second set of adjustable foot pedals below the rudder pedals; positioned properly my heels are on the lower pedals and my toes on the rudder pedals.
If I really need pressure on a foot brace when the waves start kicking up the lower pedals take any strain off the rudder control cables and I can lock firmly in place with a 5-point stance, lower pedals (2), knee pads along the cockpit coming (2), back band (1).
BTW, all of those decked canoes have a raised, single bladable seat, retrofitted in the 70’s “European-style touring canoes” (nee kayaks). The seat in the Kamerad is a Wenonah slider, the same height used in the Prism.
If your desires are for a partially decked hull for use in rough open water I consider cutting down the stern sheer along the lines of all of the manufactured decked canoes designed for open water, and consider later adding a rudder if that seems advantageous for quartering wind control.
Apologies for the verbosity; I am (obviously) a huge fan of decked touring canoes for rough open water paddling.
EDIT: Some kayakers prefer a skeg. I am not a fan, in part for course correction reasons Glenn mentions above. Also because I do not like having a skeg box occluding gear storage, and do not like the potential of having pebbles or shells lodged in the skeg housing when beach launching.
YMMV, but I have never seen a decked touring canoe with a skeg.
