I think some key points about bore to stroke ratio are being missed in this discussion/debate. If the following SAE paper also has torque results it probably has the answer to the speciic debate happening.
Engine Combustion at Large Bore-to-Stroke Ratios
I did not want to shell out the $25 bucks or so for the paper. Even my SAE membership doesn't get them for me for free...
Anyway, from my perspective, the interesting things about bore to stroke ratio are specific output (power per liter) and (fuel) efficiency. Take a look at the following graph (source: Lecture notes Prof P.M.V Subbarao, ITT Delhi)
Here is the plenty obvious conclusion. For maximizing the specific power output at the expense of fuel efficiency a large bore/stroke ratio (small stroke to bore) is required. Note that F1 and normal passenger vehicle engines probably produce about the same amount of torque say 200 ft lb, with a bore/stroke ratio of 200-250% different. Sure torque probably is affected by altering stroke alone but the focus on torque is missing the point. Power and redline rise dramatically with a very short stroke and (as mentioned prior) valve area can go way up.
Marine engines are mentioned here specifically because the big long haul type are indeed built for maximum efficiency like heavy duty trucks.
The bore/stroke ratios of most of the vehicles you've been discussing are all hovering so close to the 1:1 mark undersquare, oversquare, whatever. However, to split hairs, the S55 engine will produce in an apples to apples way a better specific power output than the N54. But at the same time it moves down the curve quite a lot to focus on efficiency over specific output compared the the S65.