You should definitely be able to do that.. by first drawing all your visible geometry only to the depth-buffer, then drawing the subtracted object like a stencil volume, and then finally drawing all your visible geometry again to the color-buffer. Set stencil-testing for the visible pass to only allow geometry outside of the shadow volume (same as when using stencil-shadows with additive lighting passes).
Okay, I was hoping that was the case. Now for the tricky bit. I plan on having the players be able to lay down multiple holes that may intersect. The main reason I'm looking at Carmack's reverse over other solutions is because it doesn't seem to suffer from the same artefacting issues as depth-pass and exclusive-or. I trust I won't have any severe issues if I have multiple overlapping holes at different depths?