The mods work fine in single player but it breaks it for multiplayer. If you go to modified.log all mods get tagged as unknown file and until you fix that problem you can't join a multiplayer game with a friend even if using the same mods. For more information you can refer to this reddit thread I created:

https://www.reddit.com/r/totalwar/comments/ene3ml/workaround_for_hosts_game_version_differs_from/

Is there something I'm missing in the mod manager that stops this from happening so I can switch between profiles without having problems with multiplayer?