Maybe the cars I used were a bad batch of hole drilling but my experience was the forward hole lined up and the rear hole was about half a hole off of the Protocraft compared to the Kadees? I was using Intermountain cars and I just reamed the hole on the car and through bolted it. But the Kadee boxes were also a half hole off compared to the Protocrafts?
As far as the Atlas cars, as I mentioned in my other post, you can use the Protocraft coupler in the Atlas box if you don't want to drill new hole in your Atlas cars. I choose this route for now but will probably go back later and use the Protocraft boxes for uniformity.
I agree about painting the inside of the boxes. I wish they would have molded them in a matte black, but o'well, at least they made them.