I've done a little work in Catia but I don't know that much about "Powermill".
I currently work in Solid Works and there is a 3D resin plotter available on the market (perfect for any type model). I assume that your doing a similar set up by uploading the 3D drawing to the machine tooling queue and then machining a resin block. Or if your doing something different please explain?
As for the changes and modifications you are correct that doing them in a 3D model is about as accurate as you can get. Plus any changes can be "test fitted" in you computer model!
Keep up the great work!