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.
Interestingly, the study simultaneously staters that the players couldn't identify the older violins but also generally rated them lower. I'm wondering, was there something different about these violins that they didn't like (indicating an identifiable, if unfavorable, difference), or did they feel the old violins just sorta came up short in a non-descript way?
Playing style and tastes have changed over the years, so that could be a factor.