Nope.
If the taper is straight then use the chord at half span. Do include the flaps on both planes, if they're there.
Well, really, to compare the CG points, technically, one should determine the CG relative to the mean aerodynamic chord (MAC) of each aircraft. Of course, the MAC of a straight non-tapered wing is its chord throughout the span. Also, for the relatively small taper ratio's usually found on our CLPA models, the MAC is not much different than the average chord. The higher the taper ratio, the greater the difference between the average chord and the MAC. If one is really wants to compare the CG of one model to another, then to do it correctly, it should be done by comparing the CG's relative to the respective MAC's.
Keith