I just want to point out what Einstein explicitely stated about that question, at least in the beginning years of GR. He merely stated that, since the microscopic constitution of matter was not known yet, it could not be incorporated to the energy-momentum tensor, and thus the macroscopic treatment of matter as a continuous medium was only a provisional workaround. He probably thought that in the future, it would be possible to include atoms individually in some form to the field equations (bear in mind that General Relativity was released in 1916; at that time, Heisenberg was in high school and Rutherford had not done his experiment yet).
Look a this excerpt from the Princeton lectures (1921), published in english as "The Principle of Relativity" - A. Einstein (available for free at the website of the Gutenberg project). When departing from Poisson's equation in his heuristic search for the field equations of GR, he states:
But our investigations of the special theory of relativity have shown that in place of the scalar density of matter we have the tensor of energy per unit volume. In the latter is included not only the tensor of the energy of ponderable matter, but also that of the electromagnetic energy. We have seen, indeed, that in a more complete analysis the energy tensor can be regarded only as a provisional means of representing matter. In reality, matter consists of electrically charged particles, and is to be regarded itself as a part, in fact, the principal part, of the electromagnetic field. It is only the circumstance that we have not sufficient knowledge of the electromagnetic field of concentrated charges that compels us, provisionally, to leave undetermined in presenting the theory, the true form of this tensor. From this point of view our problem now is to introduce a tensor, $T_{\mu\nu}$, of the second rank, whose structure we do not know provisionally, and which includes in itself the energy density of the electromagnetic field and of ponderable matter; we shall denote this in the following as the ``energy tensor of matter.''
By the way, these lectures are a very nice text. The 1916 paper is dense and challenging, but that lectures are full of heuristics insights, and the form of the equations is closer to what we are used to, in the literature of today (at least in index form).