Bizarre, really, all this talk of compressible flows and gas laws, yet a basic failure to visualise a simple physical fact.
At least in my postulated simple engine an induction stroke takes in a fixed volume of gas. Say 1ltr, This has come in through the intake duct at temperatures, pressures and velocities determined by the intake conditions, but in the end, when the intake valve shuts there is 1ltr of inducted gas in the engine. Later, at TDC on the exhaust stroke 1ltr of gas has been expelled. The exhaust gases have departed down the pipe with temperatures, pressures and velocities determined largely by the combustion conditions and the dimensions of the exhaust duct.
But the clear fact remains. The engine took in 1ltr of assorted gases and discharged 1ltr of assorted gases. This and RPM determines the volume flow through the engine. This would be confirmed by measurements of flow factors in the intake and exhaust ducts, but volume flow would only be available from calculation from velocity, temperature and pressure measurement.
And I do not dispute that this will not apply absolutely to more developed engines, but swept volume and RPM will remain the dominant factors in determining VOLUME flow
Dick