We need a way to tell if something is a mod. This could be done by making modded files have a different colour in selectors. This can help when trying to figure out if a mod is breaking something or when trying to make a scenario that doesn't require extra mods installed.
Considering mods can vary from maps and vehicles to individual parts or changes to scripts, I doubt it's possible to do this in a clear manner. Simply disabling all mods in the mod manager while you're working is also easy enough that I don't see much added value.