this sounds like you're assuming the mod launcher will always be there. from what i understand, that is made and supported by a user who has no obligation to keep it working if they choose to quit entirely.
Thing is, using Ravenhearst mod as an example, many mods have custom pois. can't have a generated world BEFORE the mod with custom pois is placed in, or those custom pois will never load/show up
If I'm remembering correctly, %appdata% and all its contents are also hidden. the average user/player is gonna have twice the trouble of locating, much less adding files, if they aren't admin user on their pc as well.