Mate I have made heaps of these, that work, and I can tell you that one in the picture would have the holes in the same spot. The difference is the hole diameter would be smaller to not cause the issue you have. I think that guy used Phillips screws to hold it. When I made mi e I used countersunk Allen head bolts and for that bolt I machined the head down so it didn't cause that issue, with a smaller countersink diameter of course. The issue is so obvious I can't believe they make and sell them as is.