Another reason for lower numbers when sweeping at a faster rate is inertia. Unless this is corrected for somehow by the dyno. I understand that if both manifolds are compared at the same rate this does not apply.
That is true. Slowing down the acceleration rate negates (to an extent) inertia. In the car you will see that inertia. That’s why you have to set up your dyno testing to duplicate as close as possible what happens in the car.