Has this thing been added to Version 4

Lets say I have two folders on my system named "Downloads" and I want to perform different rules on them. Before that was somewhat annoying, as you had no way identify them other than "reveal in finder" or rename one of the folders.

I would really love if there was a way to label the folders in the preference window so that two identically named folders would appear different. Is this possible in the new version?

No, but you can give them different icons in Finder. Hazel should show those icons as well.