Infernal combustication engines work like this.
2 engines.
Identical compression ratio, combustion chambers and piston crowns etc...
10 units of energy (thrust) in the combustion process
Engine A has a 100mm bore and 50mm stroke.
Engine B has a 100mm bore and a 200mm stroke.
Each engine runs at 1000 RPM
Engine A - lower mean piston speed.
Engine B - has a 4 x higher piston speed.
Engine A - The frictional loss from ring scrape and piston sliding occours for 100mm per revolution.
Engine B - The frictional loss from ring scrape and piston sliding occours for 400mm per revolution.
The limiting factor for power is based upon the highest possible pressure inside the cylinder, the most amount of times, per given time period; thus the limit of piston acceleration and side thrust etc., are the limiting factors of the engine putting out many high pressure pulses for period of time.
Mindful of the chemical limits of combustion speed etc., and making reasonable use of the thrust and the time of that thrust in the cylinder..
Thus a big piston with a short stroke will put out more power, than an identical bore with a long stroke.
The long stroke motor will lose a significant amount of power from internal friction in the bore and the reduced amount of strokes for a given limit of piston speed, based upon RPM.
And when one designs engines the efficiency of percentages - of the increases or decreases of power at the crank shaft, based upon stroke and bore dimensions - then taking well established designed based upon proven testing - in enormous amounts of infernal combustication engines and steam engines, accurately translates directly into operating costs of the engine, and what ever the engine has been stuck into, to power.
For instance if one is operating a steam ship or engine, or a truck or trucking fleet - one of the primary overheads is fuel consumption.
While a long stroke engine (except for the modern marine diesels) loses more from internal friction in the bore and the limit of the mean piston speed in meters / minute, limits the RPM and thus the power strokes, but it develops a high torque - a bigger engine with a long stroke weighs more and has a lower power output.
With the short to square stroke motor, the results are a smaller engine, higher RPM, more specific thrust cycles per unit of time, and lower internal friction from the short stroke.
So the balance has to equate purely into the amount of fuel in, to the amount of power out.
If one is using say 100,000 litres / Kg - of fuel per day or month, then an engine that can drive the ship or trucks the greatest distance with the biggest loads, is kept on the market and the motors that deviate anything more than marginally from the optimum expectation, are eliminated from the market.
The bore and stroke issue comes down to purely thermal efficiency and TCO or Total Cost of Ownership...
Enormous amounts of engineering and testing have established these principles.
In terms of the ultra long stroke marine diesels, these are infernal combustication engines with many special features - such as water injection - to create a secondary thrust by operating the engine as a combustion engine and a steam engine...
The pistons tend to only contact the walls around the ring lands and on bearing pads, instead of the full length of the piston and they also run in a purely vertical motion with the side thrust from the crank shaft and connecting rod, taken up with the cross head.
So the bore friction is reduced to a small fraction of a piston engine that has the piston coupled directly to the crank shaft.
In terms of eking out the residual thrust from the expanding combustion and steaming gasses, the ultra long stroke marine diesels really do it.
But this is based upon their design and the fact that they do move enormous ships with enormous loads and the fuel consumption - even though it's very efficiently done, it's still very high and it's more cost effective to have an big, tall, low RPM engine that runs at a constant speed and gets the most amount of cargo delivered, over the greatest distances, per ton of fuel.
So when considering the engine design - many factors come into play in the design.
While I understand the efficiency of a short stroke motor, the appeal of building a single cylinder engine for a motorbike, with a 3" bore and a 6" stroke, and a big flywheel, for loping through the country lanes on - has enormous amounts of appeal.
But anyway...
Life goes on.