The mounting holes are set up for the Atlas couplers and boxes. The holes are threaded for 2mm screws.
You can "force" a kadee plastic box onto an Atlas car by carefully threading in a 2mmx8 screw about 1/3 of the way on the rear hole of the box, then pushing the box inward as you thread in the second screw. The box has enough play to squeeze in. You should also use a shim from MicroMark to get the coupler height right.