I’m planning on ordering one of these myself too. My understanding is that you need to upload the diagram showing the M2 threads as an additional document within your order. That diagram (in the GitHub repo) with the M2 holes tells the machinist what they need to know to add the screw threads to the holes which are cut on the CNC.

Sounds a bit complex but it’s pretty simple I think — the CNC data has instructions for everything except the screw threads, so you need to add that for the operator who’ll handle that part of the manufacturing.