Yes, the Atlas coupler pocket does come off with a little patience. Insert a flat blade screwdriver in the rear of the coupler pocket near the center where the tab inserts into the slot in the back of the gearbox. pick a side of that slot and twist and pry upwards gently and it will come off. From there remove the spring, coupler and the two screws holding the gearbox in place.
IIRC, the CZ cars may require a .050 shim to be at the correct height. there are what look like a couple sets of holes in the bottom of the car, actually only one set are actual holes. The hole closest to the end of the car and what looks like the 3rd hole from the end of the car. I tapped them with a 2-56 tap just to clean out the hole a little bit. From there, I like the Kadee 740 for this car, assemble and attach to the car. Don't forget the shim though, otherwise the coupler will be slightly higher then your other cars! I think it also hits the diaphragms as well. Been a while since I converted a few of these cars.
Now, using these holes, and the Kadee 740 gearbox won't bring these cars any closer together. If you want to bring them in and have the diaphragms touching, you'll need new holes. Keeping in mind you'll need larger radius curves as well to ensure smooth operation. I thought about moving the Kadee gearbox back just enough so they slightly touch between the cars and use the side mounting holes on the Kadee gearbox. Just need to drill new ones and tap with a 2-56 tap and you're good to go.