I don't know if the following applies to Atlas cars with 3R couplers. All but one of my Atlas cars (first one ten years ago) were bought as 2R cars with 2R wheelsets and Atlas scale-sized couplers mounted to the carbodies. But if this may help anyone:
A few days ago I spent some time swapping out Atlas couplers with broken knuckles & experimenting with KDs on some boxcars and reefers. I found that the Atlas coupler box holes will accept 2mm diameter machine screws. 2x8 or probably better, 2x10 work well--AND because they are a bit narrower than 2-56, they can be used to attach a KD box to the Atlas carbody WITHOUT drilling or tapping any new holes.