If it were me, I would use the holes that are outside the cut zone to hold down and position, possibly with additional hold down near the cut zone.
Dowel pins are cheap ($US0.24 each in 316 stainless, 12mm long) and very precise. A couple dowel pins to locate and a couple 2mm screws to hold down will do it. If you are using MDF and MDF wasteboard, you can put in the holes using a 1.5mm (or 1/16") tool, maybe 0.02mm undersize for the pins so they lightly press fit, and pretty much a plunge then tap for 2mm (M2-0.4) button head (or round heat, or socket cap head, or… )for hold down. Truss head (larger seating surface) do not seem to be a catalog item in 2mm, but may be available. I would use a washer, myself, but for rapid changes, washers are a pain. M2-0.4 button head are about $US0.22 each in hex socket drive. The tap is about $US15. for a spiral point good quality tap (the only type worth buying for through holes, if you arn’t fond of poor thread quality and broken taps) Prices referenced are McMaster, but other suppliers are similar.
Powered driver to insert and remove screws, and fast, uniform turnaround. (I would actually use a manual spiral driver, myself, for control, but, then again, I have a lot of them).
If you want a bit better dimensional control, remove the stock waste board (Nomad) and replace it with either a piece of aluminum plate (to protect the factory bed plate) in 8 or 12mm (3/8" or 1/2") or acrylic in the same. On a Shaeoko, glue it or screw it down to whatever you are using as a bedplate. Acrylic is nice because it is cheap and machines easily and takes press fit dowel pins like a champ, but before pressing the pins, you need to chamfer top and bottom. If you do not, the surface will not be flat near the dowel pin. When you bolt it down, snug, but not too tight, because it will pull out of flat. Bore the holes for the positionint pins and hold-down screws once the plate is in place.
If you are using a Nomad, the drill pattern to hold this to the bedplate is the same as the stock wasteboard, and can be done using the machine itself. The dimensions (and maybe even a CAD model) are somewhere on the CD site. I haven’t looked in a long time for where, but I grabbed it all when I got my machine.