First, the special nuts are nuts, not screws. Second, yes, they are OEM. And are far from being unique to the Atlas machines. They aren't perhaps as common on new equipment today as they once were. But if you work on older equipment including both machine tools and military grade electronics, you will run into them in various sizes.
Buying a new tool today that fits is unlikely. But making one is simple. Measure the OD of the nut. Unless you already have one that you just haven't thrown away, buy the cheapest set of 6-point long-pattern 1/4" square-drive sockets that you can find. Measure the OD's for one that is about the same OD as the nut. Mill (or accurately grind and file) both sides of the open end, leaving two tangs sticking out. The tangs need to be fairly close to being on a diameter of the socket, and centered in two opposite thickest parts of the socket. The ID should be a slip fit over the screw that the nut fits. And the tangs need to fit the slots in the nut. I've made about half a dozen of them over the years, in different sizes up to about 3/4" diameter.
You can also make a tool from a screwdriver that fits the slot in the nut when it is off of the machine by running an end mill the same diameter as the screw across the end of the screw driver blade. But the tool made from the socket is less likely to slip and damage the nut.