But the fans will not blow at the same speed, especially considering one is driven by a belt from the crank, spinning at the same speed proportional to the crank...
While the other is variable to the speed of the exhaust, and changes with both acceleration, deceleration, and even when the engine speed is constant, it will still change its speed, by either spooling up or slowing down, because of the nature of the design.
If you had said centrifugal supercharger, this idea would have a plausibility to it that others would be able to see clearly. With two separate drive systems for each boost producer, one being fixed and one being variable, there is a differential pressure created by that variance. Thus it will attempt to move to the area of lower pressure,
At any time that the intake and exhaust valves are both closed, the vacuum inside the intake will be sealed, and it will become a pressure vessel. Even for that small micro second, things will break at those pressure levels.