Thanks for your input! I'm currently using VCarve toolpaths for these projects, but it is far from optimal. Unfortunately, when I apply a VCarve toolpath to a selection of overlapping shapes, it creates a group of anomalous paths that ruin the cut (See attached). From what I understand, this is simply how VCarve path calculation works and is to be expected. Drill paths, on the other hand, do not suffer this problem. My work-around is to manually select all non-overlapping objects to set as one toolpath, then the rest are applied as a second toolpath. It's very time consuming, both in V-Carve and during the actual cut. Furthermore, it seems like applying a VCarve toolpath will trigger far more calculations than are necessary, considering I only need a single drill motion at the center of each object. VCarve toolpaths result in huge files compared to the relatively simple drill toolpaths. I just need something to tell each drill the correct depth.
I hope I'm explaining this clearly.