Ha ha...why yes, I was talking about your sharpening stone fetish, David
LOL
Certainly all of the big guys have their pearl cut on machines. I doubt if many cut them in house. It's really just best to farm it out most times. I believe PRS actually sends their fingerboards to the same outfit to be cut as well, and they just glue them in when they come back. They probably use Pearlworks. A lot of people do. They really are the best at this sort of thing and they've been doing it forever. I'm fortunate that I have a shell supplier just a short drive from my house...Masecraft. I believe they'll do custom runs too, but I've never tried it. I just buy the raw material, dot inlays and abalone rosette pieces from them.
I tried using a scroll saw. It's just not gentle enough, IMHO, and the parallelogram movement really screws things up as well. I didn't have a fun time. It also seems to want to constantly lift the MOP if you're not careful. It was a miserable week trying to get it to work for me. Some of the linear motion ones, especially the ones you can slow way down, look like they'd do a great job. Knew Concepts makes one of those too, though it's quite expensive. If that was my thing, though, I'd surely look into buying one. There are people that do inlay full time.
But most little guys just cut out any custom work by hand with a jewelers saw and bench pin. It goes pretty fast. It's crazy for repetitive work, though, because it's so cheap just to buy it if you have any sort of volume. I not only purchase my logo, they also inlay it for me in my truss rod cover. It saves me a lot of work, and I don't remember what I pay for them each, but it's not a lot. Maybe $15 each, or something like that, in batches of 5 or so. Maybe that's off a bit, but it's really not even worth worrying about on a guitar.