Right, it is a matter of the RPM vs the flame spread rate -- higher RPM requires an undersquare design (shorter stroke than piston diameter), but this is limited by the flame spread over a larger area that is also very thin. A lower RPM can work well with an oversquare design (longer stroke than piston diameter) since there is a longer period of time for the flame to spread and the piston is smaller, too.
So all else being equal, I would think that an oversquare design burns the fuel more completely.
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