As folders, no matter how you slice and dice it, are nothing else than a tag on a file, it's kind'a weird to claim that there is anything tags can't do but folders can.
There is no reason not to have (automatically assigned) tags which denote on which file system a file is, or which even represent a hierarchical relationship ("folders"). The fact that this is not done or not done properly doens't mean it can't be done.
Similar situation: Microsoft, Google and GNOME are trying to develop one UI which works on multpiple devices but are failing. Does that mean it is impossible and there is no way to share code/UI concepts between touch- desktop- mobile- and 10-feet devices? No, just look at KDE Plasma - which is doing exactly that (but a lot smarter, yes).