My 67, Dec 66 SJ built, automatic trans, does not have these holes. No dimples either.
I've spent quite a bit of time comparing a 67 GT 350 to mine, since both are SJ builds, close in dates, and torn down. I can say that when there are differences, one car will have punched holes and the other will have dimples. One example is the holes on the GT 350 for the manual trans based speedo cable. I've got dimples because mine is an auto. There are other examples, but always comes down to dimples.
I've looked at pictures for about 10 others, but only a handfull were sans drivetrain where I could see really well. No holes like yours.
Good luck. John