Hi SpicyFlanx,
Thanks for posting your question! I believe that the Paths Carving operation might be best, and it should allow you to go as deep as you want, you'll just need to create a new copy of your topographical map and lower it by the depth you want the holes to be at and put that in its own Layer Group. Then you use that layer group for your Paths Carving operation. Your paths for milling the holes should accommodate for the cutter's radius as well (i.e. a circle that's 1mm in diameter cut with a 2mm cutter results in a 3mm hole).
We've been looking at things for a proper Hole MIlling operation to do, and following the canvas would be a great option to have. It would be a great option to have for the Hole Drilling operation as well!
Let me know if you have any further questions or need help figuring anything out :]
- Charlie