Oh dear, I promised not to get into this again, but it was a Mandelson moment.
I agree absolutely that valve overlap changes things. There is then a time in the cycle when the engine is no longer delivering measured volumes of flow but has an additional flow straight through. For all other times the engine is engaged in filling and emptying cylinder's worth of gas. The gas mixture varies in the cycle, the temperature varies and the pressure varies but the one fixed value is cylinder swept volume. RPM determines how often each plug of gas is delivered.
Nothing that happens to the gas mixture inside the engine has any effect on the volume of gas passed through, measured at the inlet and exhaust valves. The gas mixture internally suffers rapid changes of volume,temperature and pressure but volume throughput from in to out is a dimensional factor, depending on bore, stroke and RPM.
Now, this is a pretty pointless argument. It doesn't really matter about volume. If you want more volume, build a bigger engine - there ain't no substitute for cubes. Otherwise, try and make better use of the volume you have by increasing the mass flow by keeping intake pressures up or by reducing losses by keeping exhaust back pressure down.
The only reason this ever came up was because the original ATPL question had "volume" in the options. I think the question is trash, but we are engaged in an internal examination of it to see if we think it valid or not.
Sorry to bug you all, I should never have tried to shift my ATPL problems on to you.
Dick