It's important to note that the phrase "heads flow the same" could be interpreted more than one way. Normally, heads are flowed on a flow bench. They are not usually flowed while bolted to an engine block, however, though the block's bore size does affect intake valve flow. If you were to bolt a given head to a large-bore block and flow that, vs. the same head on smaller bore block, generally speaking, the large bore block combination would flow more since the intake valve would be less shrouded by the cylinder wall. I say 'generally' because "big bore" and "short stroke" and so on, are all relative terms and I'm sure there exists some application with valves so small relative to bore size that they are not at all shrouded by the bore.
It is this same intake-side shrouding that has race engine builders moving intake valve guides in toward the center of the bore, or using offset dowel pins to move the cylinder head further toward the exhaust side (thereby achieving the same effect).
In general terms,
- Engine A can potentially make more power than Engine B, depending on how high the engine is revved, how shrouded the intake valve is, and just how big vs how small the bore and stroke are of both engines.
- Engine C in either big bore/short stroke config. or vice versa, will make a lot more power than either Engine A or B since it has four extra cylinders of the same bore and stroke as the other two, and therefore displaces 50% more than Eng's A or B. (If you meant a scaled-down version of A or B with the same displacement as A or B, but with 12 cylinders, then that's a different story).
- Engine B will have less Tax Horsepower. Right, Wilf?