[BeardyMentor]

My day job is implementing an integrating CNC and other computer based manufacturing techniques in existing manufacturing processes. The correct answer here is; Do what works for you. Some parts the only way to make them is to have them done on a 5 axis CNC. Others, can and should be done with a drill press and a jigsaw. It depends on complexity and the tools and skills you have on hand. If you have easy access to a waterjet, use that. but if you just need a rectangular spacer with a 1/4" hole roughly in the center, a waterjet is overkill and the set up time will be longer than just using a drill press. For each part spend a SHORT period of time evaluating your options and use what makes the most sense.

I guarantee you that not every part can be made with the waterjet and some handwork is going to be required anyway. There will be plenty of hand work no matter how much stuff you get made on some flavor of CNC.