MM DLL is the one pulled by CKAN, version 2.5.8 I believe. As for the install directory, this is a Steam install, so it kind of goes where it goes. In previous versions I had MM installed with no problems, and mods that use MM (such as KAS) worked flawlessly as well. If it were a security issue I would think that Windows would expressly be giving me a hard time about it though, no?