The auto's have a cut out as well. At least my supposed auto version does. As do all the ones I've even seen in my Ebay searches before I found mine.
On the side, next to the shifter hole... about 4 or 5 inches long and 1 or so inches high. That's it. I believe it's pretty much a straight line along the rest of the console. On both sides.
What would be great, for the original poster and myself, is a good photo of the left side of an original 4-speed console so the contour where it meets the floor can be seen.
I think the existing hole needs to be noched on each side to accomodate the shifter boot trim ring, but there might be more to it than that.