I always thought them holes were something to do with a body re-alignment jig. I think vw would have wax injected all the box and sill sections. I know when I was welding a patch on the section just ahead of the rear axle mounting plate on my mk2 the darn thing kept catching fire and there was wax dripping out to. but I suppose a bit more wax wouldn't hurt 
Some of the holes on the underside
are datum points for body alignment , they tend to be located on the chassis legs, and be approx. 12mm in diameter,
VW heavily waxed lower box sections of the body shell, which did do a pretty good job up to a point lol.
Thom