It seems to me that the question about where the energy is located is a
scientific question. Energy of a system calculated in the center of
mass reference frame of the system is mass of the system. In principle,
all you have to do is carefully map out the gravitational field of a
charged capacitor to determine the distribution of mass, and hence
energy in the center of mass frame, in the capacitor. Another option
would be to measure the moment of inertia of the charged capacitor.
An interesting aspect of the idea that energy is stored in the
gravitational field is that it must be negative. Less field means more
energy. Imagine two identical infinite uniform parallel planes of mass
separated by a distance d. To increase the separation of the planes,
you have to do positive work on the system, thus increasing the energy
of the system. In doing so, you have increased the volume of that
region between the planes, the region where the gravitational field is
zero. In other words, you have eliminated the gravitational field in
the region of space that was outside the planes but is now between them.
Since the energy of the system is increased, there must be a negative
energy density associated with the field itself.