I may be missing something you are trying to say. But the flat rate would be the very same between you and the guy on the manual lathe. The difference would be, he took longer to make the same part. You on the other hand make it faster thus earning more in the same time. The cost for that higher efficiency is the cost of the CNC. If you can't make enough of them to pay for the higher efficiency you might as well have made it on the manual lathe.
A body shop in town with one little booth and no trick equipment has the same shop rate as the shop I work at with two down draft heated booths a computer controlled squeeze type resistance welder, laser measuring system, etc. They don't do it as fast, thus we make more GP on labor. Hopefully we do it fast enough to pay for the equipment.
But the fact is, we still have the same shop rate per hour.