The difference becomes even more difficult to assess when we see composition as identity. That is to say, an object/thing/substance/etc has an essence that is defined by the existence and relations between all of its mereological parts. Because of this, composition as identity is an essentialist theory, one that makes every property of an object essential (therefore no parts are accidental).
Composition as identity also means that there are no natural kinds in the strict, static sense. There are no strict boundaries between one "kind" of thing and another "kind" of thing. Things are not "ontologically placed" within these boundaries as if there exists a metaphysical "spice rack" with little ontological containers where things can be organized.
Instead, natural kinds are fluid constraints on the very being of reality. A thing belongs to a natural kind just if it has a family resemblance with other things. Natural kinds evolve. We can see this in the biological classification scheme, as well as the burgeoning amount of elements - in the far past, there was only hydrogen and maybe helium and lithium. Because of stellar fusion, we now have much heavier elements.
These elements are natural kinds, characterized by things that act in a similar way. But these things, these atoms, can be changed. They can be fused with each other, thus losing the essences of both and creating a new essence. Similarly, biological creatures are in a long path of evolution, where there are no strict boundaries between species. No-one is a "human" in the ontological realist sense - they are just unique things that happen to operate and appear in highly similar ways. As a heuristic, natural kinds help with communication. But they cannot be used as an actual metaphysical device.
Composition as identity also brings up some tricky things with persistence and self-hood. Since objects just are their identity, and since their identity just is their composition, then any change in any of its parts and the relations between them constitutes a change in identity. Nothing persists through change.
This does not bother the universalist too much, though, as it means that although by scratching a skin cell off my arm makes a new, unique organism, it does not mean there exists a totally different organism in the looser resemblance sense (although it is a totally different organism in the stricter ontological sense). Thus persistence in the strict sense is impossible through change, but persistence in the looser sense is possible. I certainly was not the same person psychologically five days ago - I acquired new memories, experiences, etc. But I still sense that I persist in some structural way. Although the structure has been modified, the overall appearance and function hasn't changed much.