The bird is hovering in the box. The only way for it to hover is to increase the pressure underneath its wings and decrease the pressure above its wings. This pressure differential times the area of the bird will balance the exact weight of the bird.
The pressure differential may be thought of as a net downward impulse given to the air molecules by the bird. This net downward momentum will be conserved, as the air molecules bounce down towards the bottom of the box. Energy dissipation does not affect the net momentum of the air particles.
Eventually, some air molecules hit the bottom of the box, and the downward momentum of the molecules is transferred to the bottom of the box. In response, the bottom of the box pushes the air molecules up towards the bird, which the bird then pushes down again.
The compressed air below the bird may be thought of as a static compressed spring, which gives an identical upward force to the bird and downward force to the bottom of the box. The box then transfers this downward force to the scales, as surely as if the bird were simply standing on the box.
Further analysis would examine the low pressure above the bird which is like a stretched spring from the bird to the top of the box. The stretched spring pulls the top of the box down - a downward force which is also transferred to the scales.
Together the rarefied air above the bird (stretched spring pulling down the top of the box), and compressed air below the bird (compressed spring pushing down the bottom of the box) transfer the full weight of the bird to the box, which passes it on to the scales.