Can I use any reference area for lift and drag coefficient?
The reference area is chosen according to the flow profile:


For long slender bodies, the wetted area is chosen because the main drag source is the shear forces between the boundary layer and the free flow.
For relatively short bodies, the cross-sectional area is most relevant because of the much larger contribution of pressure differential between front and aft of the stream.


Directly comparing $C_D$ of rockets and aeroplanes would not be very useful, because the reference area for aeroplanes is the wing area, which rockets do not have. Indeed $C_D$ * A is a much more useful comparison, if one knows what reference area A was chosen.