In all this discussion about thrust, horsepower, torque, valve timing, etc., there has been no mention of the prop.
Thrust is not a characteristic of an engine. In a marine application, such as is being discussed here, thrust is the force generated by the total system which includes the engine, gearbox and prop. You can measure low speed thrust by mounting a tension scale (like a big fish scale) in a line and tying one end to the dock and the other end to the transom and letting the boat pull against it.
You can take two identical boats and engines (let's say Detroit Diesel 671 engines) and put a direct drive (1:1 ratio) and the appropriate prop on one boat, then put a 3:1 reduction gear and a prop sized for that setup on the other boat. The 1:1 ratio setup will have higher RPM but less torque at the prop shaft, smaller prop diameter, probably with a pretty fair amount of pitch, and would be better for higher boat speeds. The 3:1 setup would have 1/3 the shaft RPM, more torque at the shaft, a larger diameter prop, probably less pitch, to generate low speed thrust like a tugboat or trawler needs. If properly sized by the right combination of diameter, blade area and pitch, both props will absorb the same horsepower at their optimum boat speeds, yet give very different performance. The smaller, higher speed prop will have a lot more slip and less thrust at low speed. The larger, low speed prop will have less slip and more low speed thrust but not be capable of the higher boat speed of the one with the smaller prop. All this with the engines producing identical horsepower at identical engine RPM.
Assuming (perhaps foolishly) that the engine manufacturers rate their engines honestly, regarding the 2 and 4 stroke engines, both rated at 2 HP, my guess is that the 2 stroke engine has less torque but is turning at higher RPM than the 4 stroke engine to produce the same 2 HP. If they both have the same lower unit ratios, then the 2 stroke one would also have less torque but higher shaft RPM at the prop and would have a prop with some combination of less area, diameter and pitch. The result is a prop that generates less low speed thrust.
Joe