Showing the rest of the bass might explain what we are looking at here. It's obviously a 5 string. Is it a 3 x 2 headstock? How are the saddles set for intonation? As others have said, it's possible you are cringing at intentional science or artistry. I've done a couple string-through conversions and it wasn't hard to get the holes in perfect alignment, but at least one of the basses I drilled needed the holes to be staggered for allowing greater rearward movement of a couple saddles to achieve proper intonation, which is necessary for some types of strings in specific gauges.
After all is said and done, and as Jimmy M said; stringing through the body really doesn't change anything anyway, so perhaps the bass simply has an intentionally built-in feature you won't use.....
After all is said and done, and as Jimmy M said; stringing through the body really doesn't change anything anyway, so perhaps the bass simply has an intentionally built-in feature you won't use.....

