Having done inlay work myself I can tell you this. For production guitars they are likely milled using sophisticated equipment with incredible precision capability. It wouldnt make sense or be cost effective to do them by hand.

For hand inlay work there are :Tricks of the trade.”

1. If you notice almost all inlay work is done on dark wood. Theres couple of reasons for this. 1. The contrast makes the inlay work stand out. 2. The edges can be filled in with a sawdust and glue mixture that can be sanded down and become virtually invisible.
2. Use the right tools for the job. Cut MOP with a jeweler's saw. Always wear a mask when cutting or sanding pearl. Failure to do this can result in permanent lung damage. This is not a joke. Be safe when working with pearl.
3. Save your wood saw dust in a clean container from shaping and sanding for your only work.
4. If you cut your wood about the depth of a razor blade (not edge) deeper than hour pearl. You can sand it after tac glueing your inlay in place the saw dust will fill in around your inlay. Then pour a very thin glue around the edges. Your saw dust will harden and make your inlay look almost perfect.

And That's how it's done.