Grayrock knows more than I do, but remember that this "system" of marking was used by gunsmiths and armories around the world, and not just confederate gunsmiths. All these guns made with non-identical parts were fitted together, and once fitted, the parts were often so marked so that they could be put back into the same gun once disassembled. Northern workmen did this, and Southern workmen did this, and workmen in Europe did this, and so on.
Sometimes they used real number stamps, and sometimes just used a flat blade screwdriver to make Roman Numerals such as III or VII and so on.
If Grayrock says that the US conversions done by the federal government in the 1850s don't have such marks, I don't know differently, and I don't think he would say it if it wasn't correct!
But often sellers will tell you that such marks are a sure sign of confederate work, and that's an overstatement.