In this instance I had made a custom jig on the mill which got clamped to the side of each box. Both left and right sides received holes. Sometimes the same, sometimes different (multiple jigs).
The work flow was roughly:
1) clamp jig to appropriate side
2) grab drill #1.
Drill a single hole
3) grab drill #2.
Drill three holes
4) grab drill #3.
Drill a single hole.
Eventually two different size c-sinks would be used to debur some holes, while the belt file handled larger ones
and so on.
Flip box to opposing side and repeat.
Plugging and unplugging cords every 5 seconds would be....amusing.