An engine produces peak torque at the rpm where it is most efficient. Efficiency is the result of many factors, including airflow, combustion, and parasitic losses such as friction and windage. Comparing two engines with the same displacement, a long-stroke/small-bore combination is simply less efficient than a short-stroke/big-bore combination on several counts.
Big bores promote better breathing. If you compare cylinder head airflow on a small-bore test fixture and on a large-bore fixture, the bigger bore will almost invariably improve airflow due to less valve shrouding. If the goal is maximum performance, the larger bore diameter allows the installation of larger valves, which further improve power.
A short crankshaft stroke reduces parasitic losses. Ring drag is the major source of internal friction. With a shorter stroke, the pistons don’t travel as far with every revolution. The crankshaft assembly also rotates in a smaller arc so the windage is reduced. In a wet-sump engine, a shorter stroke also cuts down on oil pressure problems caused by windage and oil aeration.
BINGO!