I am having a similar issue. I decided to run Skyrim, SkyrimSE, and Fallout4 thought 1 instance of MO2. Everything works (TES5Edit, SSEedit, Body Slide, Etc ) except LOOT. The application runs yet only the base game elements are displayed, not any of the mods. As the mods are now housed in the user/appdata folder by MO, is there an argument I need to add so that LOOT sees them? I tried setting the "start in" field to "C:\Users\John\AppData\Local\Skyrim\mods" but that didn't work. Any ideas?