"Among all the countless things and classes that there are, most are miscellaneous, gerrymandered, ill-demarcated. Only an elite minority are carved at the joints, so that their boundaries are established by objective sameness and difference in nature."
(Lewis, David. "Putnam's Paradox." 1984. Reprinted in Papers in Metaphysics and Epistemology, 56-77. Cambridge: Cambridge University Press, 1999. p. 65)
That is, natural (non-conventional) classes are identifiable in terms of (observable) objective resemblances or similarities between things. But since there are different degrees of resemblance or similarity, with things being more or less similar to each other, there are also different degrees of naturalness: not all natural classes are equally natural; some are more or less natural than others, with some being perfectly natural and others being imperfectly natural. A perfectly natural class is one whose members are qualitatively identical, i.e. (intrinsically) indistinguishable duplicates, such as the class of electrons: every electron is perfectly similar to any other electron. The classes of elementary particles and the ones of chemical elements are perfectly natural.
Regarding the last sentence, if any electron E can have a locus assigned to it such that it can't occupy the same space at the same time as another electron E2 then it's not identical with E2.
This ontology is different from the ontology of minds and bodies. Minds and bodies do occupy the same space and time as each other because they are two aspects (perspectives) of the same. But multiple electrons aren't different aspects of the same are they?