Actually, the individuation of spacetime points is already a problem in special relativity. Again, Giulini has interesting comments in
http://arxiv.org/abs/0802.4345 , the part "From a General-Relativistic point of view, Minkowski space just models an empty spacetime, that is, a spacetime devoid of any material content. It is worth keeping in mind, that this was not Minkowski’s view. ... Even if the need to incorporate gravity by a variable and matter-dependent spacetime geometry did not exist would the concept of a rigid background spacetime be of approximate nature, provided we think of spacetime points as individuated by actual physical events."
I agree particularly with Giulini's comment "If we mentally individuate the points (elements) of spacetime, we—as physicists—have no other means to do so than to fill up spacetime with actual matter, hoping that this could be done in such a diluted fashion that this matter will not dynamically affect the processes that we are going to describe." - except that I would say "experimentally individuate" rather than "mentally individuate".
In other words, the metric in special relativity corresponds to matter. In Maxwell's equations on flat spacetime, the metric corresponds to electrically neutral measuring rods. Although real measuring rods are composed of electrically charged particles, those clump together so that on the scale on which Maxwell's equations in flat spacetime are true, the rods are electrically neutral. In general relativity, there is no such thing as a measuring rod that does not interact with other matter, since mass couples universally via gravity, and the metric becomes dynamical.