this might sound odd but why not have 1 sub option for everything with a core app that changes how mods are managed to allow for the individual mods settings.

Also part of all these mods is that they add so much clutter for research and are hard to keep in mind of how they work, it would be nice if we somehow got something like the steam workshop explanations (with the pictures and arrows showcasing) in game. I don't know if that would help, I am just brainstorming ideas.