2mm x 8mm screws are very easy to find and buy in real hobby shops or on line. The holes on the Atlas cars, new Atlas are tapped for 2mm screws. So just enlarging the rear hole on the coupler box gives you a 2 screw mount with correct threads.
The problem with drilling and tapping new holes is that you only have to move one hole a few thousandths of an inch. So the new hole would essentially be elongating the old hold on new Atlas cars.
Also most of the New Atlas cars do not have plastic underframes. They are cast zamak and fairly hard version of the alloy. They do hold threads very well.
The original "old" atlas from the 80s have holes sized for Kadee boxes. They do mount the box sticking out a bit, so you could drill new holes to remount them closer. Otherwise to use the existing mounting holes you can push a 2-56 nut into the inside hole on the frame which is sized for it and then mount the couplers with 2-56 screws which are even much more common than the metric screws.