Yes, the tools run outside of MO and even pickup manually installed plugins. And no, the proxy is not used for FO4Edit, xTranslator, BodySlide or Loot (those are the tools i try to run). i replaced the EXE of the Proxy to see if it fires (it at least creates a log if it was stopped before it shows it's GUi) and so far it was only used for those tools. i even tested Explorer and MO detects that it is Explorer and injects the DLL directly, not using the proxy (Explorer ofc crashed with a memory exception). So far i replaced the proxy with my own version that creates SymLinks based on the mod order in MO and got my tools working this way and as launching the game does not call the Proxy executable no SymLinks are created making it perfectly safe to use ... so far.