Hi, thanks for the review. I added a Show Overlaps
button that will highlight the overlapping vertices (by selecting them) without merging them. You just need to be in Vertex Selection mode to see which vertices are highlighted. I'm not sure if this will address your exact issue, but hopefully it will be helpful. Just update to version 1.1.0 for that new feature.
Awesome addon! I was looking for something that will at least partially replace xview from 3ds max. However, i think it misses one important option - to just select those overlapping vertices instead of merging them. Its usefull in cases where the vertices are from different meshes, and should not be merged, just moved a little.