I'm not sure what you mean by "determined separately". Computed during design phase or checked when the prototype is already built?
I recall that during my flight mechanics classes in university, in static pitch computations phase, we were indeed starting with aero characteristics of the wing alone (center of lift included) to compute the pitch moment of the complete wing, then added the moment caused by the fuselage and/or nacelles (based on RAE ESDU reports, we've been told that typical fuselage usually moves CoL of the whole airframe by 2 to 5%), then added vertical stabilizer to it (ESDU report again).
For the wing computations we were using the CoL position given for 2D airfoil only, we did it just for the sake of simplyfying the task - not so much of an error if you have a rectangular wing anyway. I suppose things get a bit more complicated when you have a trapezoidal or eliptical wing, but I really don't know how strongly such a wing planform affects the position of the CoL for the airfoil.
Cheers.
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