Agreed the extra holes are for electrifying a bulb, but I can't think of any production item that even uses just the base for that sign. Why would Lionel set-up and punch the extra holes, with no application for them.
The LL Jr bases look the same, size, shape, mount holes and metal gauge, but no electric application on the Jr signals.
Since the extra holes would be a separate operation from the blank or form process, they would have had to be done deliberately.
I hate to guess at these things, but possibly something illuminated may have been planned for that size base, pieces were produced, then used for regular production.
I can think of several Marx items that have slots or holes for features planned, but never made regular production. The 3556 scale series caboose was planned to be illuminated with marker lights. Early examples have the marker holes, but it was never made with the markers. Eventually the 2 punches were removed from the tool and the holes disappeared.