In aircraft design, wing loading (W/S) is a parameter useful in describing where is a particular design(aircraft) with respect to the pertinent design space. This term is simply the reference weight of the aircraft divided by the reference wing area. Other parameters are aspect ratio, thrust to weigh ratio, wing thickness ratio, etc. These terms are used mainly to compare designs. However, the performance of the design specified by such parameters has to be calculated, simulated or flown at a specific C.G., with the performance effects resulting from that c.g.! So, C.G. location many times becomes another useful design parameter (like wing loading, aspect ratio, etc.) in preliminary design studies, where we may be looking at various degrees of flight control sophistication (for example unstable fly-by-wire versus a purely pilot-dependent system).

Yes, the wing is "loaded"differently at steady state flight conditions, depending of C.G. location, control geometry, etc, thus affecting trim drag polars , blah, blah, blah. But that is not the use that the more well-known "Design" wing loading term is intended for.

The former is more of a "average" or "macro" term used in comparing airplane designs, while the latter is used during a "fine tuning or detail" aspect of design process.