That makes sense. In that case, you should probably just auto-populate all of that with every install, and disconnect them from the auto-import feature.
Or even make it an option on install? "Auto populate game folders with well known naming convention" (yes/no) or something. That way the behavior is clearer to the user as to the intent behind it.
I have my entire game library completely outside of LB, so all those folders aren't relevant to me. Although with the auto-import feature and naming conventions I may reconsider that. I'll have to give that some thought.