To find a perfect, and I mean perfect case is nearly impossible at this point. I've bought, upgraded, and sold nearly 150 Cubes by now, and have only come across 2 perfect, 10/10 cases. The only reason they were perfect is because they were in their original boxes, with the factory foam around the Cube to protect them, and then the factory plastic that is stuck to the Cube itself. If they were ever used, even by the best owner, they will have some kind of mark. The acrylic is so soft even using the finest diamond paste and buffing still leave trace marks at the right angle. You have to be looking for it at that point but perfect means flawless so it's easy to find the imperfections.
Also, as you mentioned with your Cube the top screws were notorious for cracking. That is actually a major reason why Apple discontinued the line. I'm sure Steve freaked out when he heard reports of that happening. He did have a major affinity for the Cube style design so I think he definitely took that personally. I mean what other Apple product can you think of that was know to have a major physical defect from shipping alone? Even in their very well made box, and shipped by the best courier they still cracked. The entire weight of the Cube is resting on two pressure points, especially when on it's side, that were 1/4" wide each. The metal top screws aren't going to give so naturally the first thing to do so would be the acrylic case. Either way, enjoy your Cube, they're the best.