I think the problem is that Dr Stupid is taking "inertial mass=gravitational mass" to be exact. It is exact in Newtonian gravity.
However, in GR, inertial mass is not a fundamental quantity, and neither is gravitational mass. One could ask, if a mass follows a geodesic exactly, even if one includes backreaction of its mass on the background. If the backreaction is not included, then its mass is not gravitational.
Usually to avoid this problem, the weak EP is not formulated as "inertial mass=gravitational mass", but closer to what Dr Stupid is referring to as the Galilean equivalence principle. For example, http://relativity.livingreviews.org/Articles/lrr-2006-3/ section 2.1.
Also even if one uses universality of free fall, I think it is only true to some approximation in GR (due to backreaction problems). That's fine, since the EP is only local. However, if one states the EP as minimal coupling, then it is exact in GR.