Even if you imagine doing them separately, the acceleration of the Earth cannot be calculated based on just a singular force unless you assume nothing else is exerting a force on the Earth during the process of the fall. For a realistic model, this is a bad assumption. The Earth is a massive system which interacts with a lot of different systems. The one tiny force exerted on it by either the feather or bowling ball has no measurable effect on the motion of Earth. This is not just a mass issue, it's the fact that Earth's free body diagram would be full of Force Vectors and only one of them would either be the feather or bowling ball as they fall.

As for my second point, I understand your model and I am defining these references frames by talking about where an observer is located. An observer standing still on Earth would measure the acceleration of the feather or bowling ball to be 9.81 m/s/s. If we placed a camera on the feather or bowling ball during the fall, then it would also measure the acceleration of the Earth to be 9.81 m/s/s. There is no classical way that these two observers would disagree with each other in the magnitudes of the acceleration.

Think of a simpler example. A person driving a car towards someone standing at a stop sign. If the car is moving 20 mph towards the pedestrian, then in the perspective of the car's driver, the pedestrian is moving 20 mph towards them. There is no classical way that these two speeds will be different.