Carol has shown me the difference between a $10 tube of oil paint and a $100 tube. You're right though, two different instruments, same model, made in the same factory on the same day can be very different. But the tube of paint is going to be pretty consistent every time.
I don't know about the classical instrument thing. There is obviously a big difference between a million dollar violin and a thousand dollar violin, but I wonder how many of us could really hear it (or appreciate it) if we're not classical musicians ourselves?
In the guitar world there's a law of diminishing returns, so there isn't that much difference between a $12,000 custom shop Les Paul and an "everyday" $3,000 Les Paul you can pull off the rack at your local Guitar Center. And a $300,000 1959 Les Paul does not sound or feel or perform 100 times better than that new, off the rack Les Paul. I don't know anything about classical music instruments, but I have to imagine that there's a law of diminishing returns there too.
Of course if someone says to you, "Look at this, it's a two million dollar violin, listen to how beautiful it sounds," and then they play it, you're going to think, damn, that does sound good! Same thing with a 1959 Les Paul. But I'm pretty sure no one here can listen to a record they've never heard before and say, "That's a Stradivarius," or, "That's a '59 Burst."
But again, if anyone wants to gift me a 1958, 59 or 60 Les Paul...