At first glance, two violins should sound different from one another, at least hypothetically. They are made from different pieces of wood, they can have subtle variations in dimensions (such as the graduation of the plates), and so forth. At an extreme, one of the instruments could have worn-out strings.

It doesn't seem outside the realm of possibility to make physical measurements to find out whether these differences are likely to be borne out in audible ways, e.g., by looking for differences in resonances of more than a few dB.

What would surprise me, would be if such studies uncovered no differences, because it would mean that the luthier's art has been refined to an exceptional level, in order to make instruments sound the same.

Now, if it's possible to discern a difference, even without being able to identify the source of the difference, then it becomes a completely different matter, which is, which one sounds better? And that's a subjective matter.

Disclosure: I'm not a violinist, but a double bassist, and in the world of basses, there are profound differences in materials and construction among instruments, so the idea that two fine instruments should sound different is quite plausible.