:Is there any particular (structural perhaps) reason that canoes and open boats are cartopped gunwales down?

Yes! On an open hull boat its best to haul upside down. The guwales and vertical sides distribute the load along the full length of the hull. This is similar to a steel I-beam. Upside down the load is carried by 4 stable points instead of trying to balance on 2 points along the keel. Another thing to consider is that right side up the air stream will tend to lift your boat away from your car rather than press it down. To haul a boat right side up (as on a trailer) you need rollers or padded skids to distribute the load. Check with your boat designer for reccomended support locations and sizes. (this is critical to avoid overstressing the hull) I know that hauling my Grumman canoe on the keel voids the warranty.
Until you can get a trailer, make a temporary frame from four 2x4's, Two going accross and two running lengthwise to stap to your cartop rack. Add some plywood gussets and carpet, and head for the water. I've seen the picture's and I doubt that anyone will notice an ugly rack.
P.S. please re-post your website.