The soft jaw fixture has through holes to guide the drill from the top flanges to the bottom flanges, and is designed to fit in a 6 inch Kurt vise. The soft jaw was printed with a cavity exactly the same size at the part, so it's a very tight fit. Adding .002-.005" of clearance on a side would make this a lot easier to use. That clearance might also make up for waterjet taper if the flats were waterjetted and then the cross holes were drilled.
I mounted the jaw in the vise, pressed the part in, and closed the vise jaws.
The part took some prying to remove from the jig, but the soft jaw held up nicely, and the PLA had just the right amount of squish to allow for variation in the part. If you need to drill cross holes in waterjetted flat, this could be a helpful workflow.