I don't know how PP would feel but IMO, you altered it and it's now yours. If I was the seller and you had NOT sanded and glued the edges. I would be happy to issue a refund. But once you did that, it's yours.

You could call the manufacturer and tell them you bought a chassis and it has a hole that's not counter sunk. I wouldn't tell them you bought it from a 3rd party though. And you might have to be creative and tell them your hamster ate your receipt or something.