No, Microsoft's (at least from watching it with Regmon) does the same thing as they all do:  recursively walks the tree, looks for stale or dead links, prunes them.  It parties right down into third party ISV sections as well, so its not based on any secret internal Microsoft data. 

 This isn't rocket science.  You could do the same thing (metaphorically) with a phone book by going through and calling every number, verifying the information, and crossing out invalid entries.  There's neither magic nor malice nor misrepresentation in a basic registry cleaner, they do a useful function.  As for the 50 of them out there that do nothing but sell you the privilege of removing their advertisements, that's another story...