im not talking about just the fuel burn in the chamber. If the clearances on the bottom end are tighter its going to take more effort to rotate the crank (not much, tighter clearances are better in fact), as well as the rod stroke ratio.

now I dont have to explain the advatages of leverage to you. It takes engergy to spin an engine around....and remember its not just turning the crank, youre compressing other cylinders, exhuasting gasses, and suckin in fuel on other cylinders all at the same time. Now with one cylinder fully compressed, there is only so much potential engergy that can be stored there. The more resistance your engine puts on the crankshaft rotation, the more of the potential energy will be eaten up. Measure this resitance in time and effort, it takes longer to push the piston down because it takes more effort. When it uses more effort, you loose some output. Thats where the hypothetical circumstance comes from.

So now like P51D said, the shorter the rod the further the piston will be down the cylinder at 90* rotation on the crankshaft, getting intake air velocity flowing faster, thus filling the chambers better at lower engine speeds. But your power band is shorter, although maybe lower down, than an engine with the same stroke. Same thing goes with longer strokes, but becomes even more drastic.
With longer rods and the same stroke your power band may start a little later, but it is longer (up the rpm range) and smoother (flatter).
You can make up the differences to some degree with intake tuning (runner length and diameter) and cam selection.
PF, youre right. The more air/fuel in the cyinder, the more potential energy is being stored...weather it be more bore and less stroke....or less bore and more stroke.