I believe the problem was simply that the normals were being calculated based on the split up edges, and it was happening in a "stair-step" pattern causing the edges of some of those "stairs" to go black. I suspect that DarkPlaces recalculates normals on load and even looks for co-locating vertices that aren't attached to the same triangle. Or something.
Here's a screenshot that sort of shows the funny stairstep:
And here's bomb.mdl: