The center of mass of a closed system can be considered a point where all mass is concentrated. Any external forces that act on the system (like the scale pushing up from the earth in opposition to the weight of the box) effectively act upon the center of mass. The position of the CoM within the system (which is not necessarily the CoG, though on Earth I suppose it would be) is irrelevant in this case. What counts is the vertical component of its velocity
The rotor downwash has no measurable effect on the outside of the box, since energy cannot enter or leave a closed system.
Can't say I'd mind a heli for Christmas either, though
