Yeah, its a bit of shame. It wouldn't be hard to make a clamp on template - one for pilots one for final sizing to ensure it was bang on. Obviously whatever method they are using in the factory isn't working. Its not just out of line, the spacings between them are different as well. Currently trying to decide if I can get away with just filling and redrilling a couple of them rather than all of them. Hopefully I'll get a bit of time this afternoon to have a look.
It was suggested that the washers etc would cover the holes if I just elongated them a bit, but that fix doesn't really appeal to me as I will know there are gaps underneath.
I've tried pretty hard to back off my perfectionism in recent years as it can get in the way of enjoying stuff like this, but my whole job is fine detail, so its hard when I see stuff like this.