During the process of optimizing the meshes and maintaining material ID consistency (see previous post), I was merging verts based on a distance threshold, which while good, was still leaving a fair number of coplaner verts. For example, the verts on the right would be merged, but not the verts on the left.
In order to solve this, select all verts (from every fragmented piece), press delete, choose limited dissolve, and set the angular threshold. A value of 1 will suffice without compromising the silhouette of the individual fragments.
Using this technique in addition to merge verts by distance, I was able to reduce the vert count from ~45k to ~30k on the trough mesh, which is quite a reduction :).
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