Inner Trunk Bracket?

This is probably a stupid question. The innder trunk brackets have two oval holes for your bumper to bolt through and then one other 3/8" or so hole that doesn't appear to have any useful purpose? I went to a car show yesterday and checked out a trunk and there was just silicone in it? I was just going to weld it up unless there's a reson for it. The trunk seems to have numerous similar sized holes in the drop down area where your gas tank goes, why?
 
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they were alignment holes for when the car was assembled . there are several of them all over the car . such as the outer flange of the cowl and in the engine compartment in the front of the cowl on the flange and the side panels under the front fenders . they were filled with a putty or tar. there are also notches used for alignment .