Why should the game scan the root folder?
And even if it does, it won’t get confused by additional files there. It scans for files it expects to be there, not random stuff.
Auto-update of mods is not always a good idea. If mod A depends on mod B, and B gets changed in a way that makes updates of all dependencies necessary, auto-update ruins my game. If I made personal adjustments to a mod that get overwritten by auto-update, my game is ruined. If I don’t like a particular update and would like to keep an old version, auto-update deprives me of that option.
If I heavily mod a particular game (as opposed to installing like 2 or 3 minor things), I tend to avoid the Workshop even if it’s available, for exactly that reason.