I've seen a picture on here of a similar pickup casing hole. Probably the casing was stamped out from a flawed piece of metal and the factory QA didn't pick it up. I'm sure Adam changed it as it's certainly not what it should be. You always have the option of taking the casing off (it should be held on by some solder either side of the baseplate) and having an uncovered pickup. But I'd be more prone to replacing the pickups anyway.

You could try staining the fretboard if the two-tone wood is putting you off. Manufacturers do it a lot on cheaper guitars as they often use non-consistent colour boards and then stain them dark to avoid wastage.