Yes, I always thought the same about the pickguards and remove them.
I attached a photo of another one I have, it's not nearly as pretty but it's interesting. It was a limited run standard but has an ebony fretboard and it came standard with no pickguard so it doesn't have the holes.
I remember when that buckethead LP came out, larger body, Killswitch button and 27" scale. Was always curious about it.