That's right. You noticed it too huh?
Yes the holes are pre-drilled, and they're not quite aligned. Same with the pickup cavities. I figure it's not going to be noticeable when played and way too hard to correct. It's not noticeable from just the holes, and I didn't install the post mounts until the finish was done. By then it was too late to do anything about it.
The bridge is about 3 degrees off straight, but otherwise fits ok.