The biggest problem you have is the thinness of the veneer. In all woodworking, the finer the grit wood is sanded with, the lighter the finish will be. Since you have no real idea of what the manufacturer sanded the finish veneer of the ply with, you could sand with a finer grit, and create a noticable light spot - assuming you can get rid of the scratches with out going through the veneer in the first place. You can also just make it worse. Or.. you can gamble and give it a try. You can always veneer over it with a matching piece from a scrap of the ply - but even this might be more of an eyesore than what you have.

You're between a rock and a hard spot. I unfortunately think you're going to have to live with it or doctor it with some decoration etc. When you build things , you're very close to it and tend to obsess over things that really arn't that bad.