This has been one of my favorite book series for many years. It has been a while since I read the first one. I will say that the language hasn't aged all that well, but the story is still imaginitive and a fun read, with a hint of proper existential dread. I do think that the books that follow it in the series are better.
On my Prusa's there is a pause command. The Artillery should be using Marlin (unless you flashed something else). Your slicer (Cura especially) will let you add a pause and even tell the machine where to park the head, that doesn't use M600. I guess it depends on your firmware and the slicer you are using. It would easy to experiment with it. Put down a small test cube and add some pause commands and see what happens. I would use Cura or Prusa Slicer if you can as they both have pretty good support for the typical commands you would use on this.
When I make magnets on the printer. I create voids the shape of the magnet in the model near the bottom surface, then have the printer pause right before it the layer it is set to close the hole. Drop the magnets in and resume print. It will completely encase the magnet.
If you are up for suggestions. I would swap filaments at the layer after the base is finished and switch colors so that the logo will pop against the base color.
Feel free to advocate for the books you'd like to see here in the comments.