Surface area of the piston affects the burning, once the burning is done, it's the cylinder pressure that pushes down on the piston... The mixture does not burn for the whole stroke, but just until all of the gasses are burned and the efficiency of the burning... Once the gasses are burned, the pressure in the cylinder is what pushes the piston down...
Now when the piston is at mid stroke, the crank is at 90° which is the pure definition of torque - force times perpendicular distance... The longer the stroke, the more perpendicular distance, hence the greater torque generated...
Also at mid stroke is maximum side load on the piston as the force is maximum when the crank is at 90°... That's why most cylinder wear is measured at mid stroke in the bore... A longer stroke with the same rod length will increase side load on the piston and cylinder wear...