The video you linked has a number of parts on a fixture to position them. The machine will have a means of absolute positioning and tool length compensation, as does the Nomad, but the fixture is likely mounted on the machine with registration pins (or stops, or other positive locating means) and was likely cut on the machine itself (not the only way, but the easiest and usually most efficient way).
For a one-off on a pre-molded case, there are a lot of options, and my first choice (in the absence of a fixture system) would be glue a piece to the wasteboard as a stop, machine the stop as an L shape, to be parallel to the machine axes and at a known position so the part can be butted in both for X and for Y, and then tape down the part butted up to the stop. (No matter what software is used for the features n the part, this is a good starting point). I have done a LOT of parts this way. Easy and cheap. For follow up work on existing parts, I often set up a straight edge stop for position and orientation with one axis, and a single pin for the second axis (the bed plate setting the third axis and other two rotational constraints, for the total of six degrees of freedom-- X, Y, Z, pitch, roll, and yaw).
Your thought of milling the profile into the wasteboard is a good one, but the likely result will be either too tight for the part to fit or a sloppy fit that is equivalent to mating two side only. A perfect fit pretty much requires modelling the part perfectly, then cutting the negative with extra relief as needed (corners, for example) to avoid binding. If the part is not a perfect match for the model, you gain no advantage. [I use this technique when doing parts that need repositioning during the job (two or four sided work, for example), as I can be sure that (barring a bad tool size) the cut will match the part.]
As for the features you want to machine, there are a lot of ways to do it. Based on my general workflow, and the need for the notch, I would do this in Fusion360 (or Inventor, but Fusion360 has more features without spending money) by modeling the part, then the holes and slot, and then using the CAM component to produce only the features needed (bore strategy for the round holes, and slotting for the slot), without worrying about a perfect scheme. Let the tool cut air for a while. It doesn’t matter for a one-off. I thnk this could also be done with Carbide Create, but I do not use it, so I can’t give any suggestions there, but I am sure others here can.
Fixturing is an art and a science, and I have about 0.75m of bookshelf dedicated to books just on fixturing, and a lot of others the cover the topic as well (look up Colvin and Haas, Jigs_and_Fixtures… It is THE classic)