Yeah, that's definitely a screw hole routed into the opposite horn, no doubt for some knucklehead righty who thought it would be cool to play upside down and "look like Hendrix".
You know, this is one of the biggest pet peeves of mine when it comes to finding rare lefties - hoping some idiot righty didn't f*ck with it. They have every bass on the planet to play, so why do they have to go out of their way to screw with what little is out there for us?! 
At any rate it's a fairly common mod with lefties and doesn't really detract significantly from it's value (or playability/sound, obviously). As for the extra hole under the D tuner, I'm not sure what that is. Normally you'd see such a thing if someone installed different tuners at one time that didn't line up with the old holes, but in this case it's just 1 arbitrary hole. 
