MAC
The fairings you refer to may affect the location of the neutral point but need not be considered part of the wing. There are several effects that are hard to quantify like the wake of the fuselage reducing the effectiveness of the tail and the wake of the wing reducing the effectiveness of the tail. They are usually accounted for by a fudge factor and the fairings can be treated in the same way by increasing the fudge factor a bit. The MAC usually comes into play to estimate the CG location required to produce a given static stability. I am of the opinion that the presence of the fairings is destabalizing.