All of the bullet core molds I have in my swaging kit are custom deals. Use some aluminum blocks in the appropriate size, index them so as they mate properly, and thread them for set screws for the handles.
The trick would, IMO, be to set them on the lathe and/or build a custom cutter. A custom cutter on a milling machine would be... troublesome. Best, IMO, to use a lathe with an appropriate mounting plate. Your cutting process would be in reality a boring operation, as you're going to bore out the holes. You'd be doing it with a custom boring bit vs. one of those indexable boring heads. It will be a bore! lol