Yes, the smith at Ruger who fits the grip frame and rest of the parts to the frame hand engraves the serial number or part of it on the parts. I think mine has his initials in the grip frame too but can't remember right now.
I think they go with 3 digits because it would be hard to match up another part of a different gun to the same exact serial trail. They ship guns all over the place and two ruger nuts getting together with the same ending digits is probably far off.
I know mine will never be too far from the frame anyway.