There is also the issue of combustion surface-to-volume ratios. As an example, when bore size is increased and stroke unchanged (trending toward an "over-square" engine), additional surface area is exposed to the combustion flame while piston speed remains unchanged. Given no compensation for this condition, some cylinder pressure (heat) can be lost to the cooling system, resulting in a decrease in power. A similar condition can be created by an increase in stroke while bore size remains the same.
Also noteworthy, when selecting paths to a specific parts combination, is linking valve timing and motion with piston speed (over a desired range of rpm). Again, as piston speed is reduced (during the inlet cycle), the rate of pressure drop across the induction system is decreased. This suggests valve events (particularly on the intake side) that help compensate for this otherwise reduction in flow rate and net volumetric efficiency require attention. In the end, an engine's torque characteristics (as typified by the shape of its torque curve) are a function of volumetric efficiency. Actually, absent the effects of pumping losses and removing the influence of combustion efficiency, torque curves and v.e. curves are quite similar.
These are some of the more notable conditions to consider when making decisions about how to configure a specific engine's piston displacement. In the end, virtually any component that affects piston movement should be considered in the "equation" when selecting major engine components. Today, perhaps more than ever before, parts integration and compatibility are critical to the performance of a winning engine combination.