I don't know the details of how CM will fix the skin for you, if it even will, mostly because I do them by hand.
One thing I do know is that if you are not hand painting skin verts, snapping verts should not cause the problems I was mentioning earlier. Otherwise, if you are painting them by hand, then if you snap the verts while the skinmesh is applied, the skinmesh modifier's internal list of vert-to-bone values will be mangled. So in that sense, after you weld your verts, it would be best to repaint. Again, if you are letting bone radii do the painting for you, this should not be the case, but don't quote that as fact.
If the issue is simply that that many verts are too close (as told by the exporter) then I would simply ignore those issues. That many verts really won't matter one bit. I've left a lot of useless verts on the ape faces, and that number probably is in the 50's. Unless those verts it is pointing out are part of duplicate faces, reversed normals, etc, then they are just warnings, not actual errors, once it comes to being in-game. I've never had critical errors simply for verts wanting their personal space.
If you want to check for phantom faces on your skin, which is the most likely issue you are having, given your data and all the crap I went through doing my mods with the human bodies with extra nodes, try this:
Set your model to see through via the node properties.
Hide the bones temporarily
It may help to smooth the entire skin section to one smoothing group
Now spin your camera around and look for faces that appear whiter than others near them
Given the single smoothing group, they should pop very quickly to the eye
Also look at your model from the inside, or select all faces on your skin (before the skin modifier, possibly by inserting an editmesh modifier before it) and set the normals to unified. This will take all the reversed normals and put them on the outside so they make white spots whiter.
I'll be back in the morning to help if the demons are not yet banished.