To clear things a bit more or at least I'm trying to
Independent libs, also called standalone, got an own .txt file which the game loads. Like an addon.
Where libs shipped embedded/in subfolders of other addons will just be loaded by help of the addon's .txt file itsself. They got no own .txt which the game recognizes.
The loading will be handled by the game. LiBStub is a library which tries to assure that always the newest library version gets loaded. And the game got also a routine inside the .txt files called ##AddOnVersion which does the same. Loading the newest/highest number ONLY.
So even if you got libs inside subfolders the game or LibStub will always load the newest version only. Placing and updating the standalone lib in the AddOns directory will help to always be updated. There might be constellations where older versions of the libs in subfolders of addons might break this, but I hope this will only happen if someone decides to strip LibStub from an existing library and switching to Zos routine of using ##AddOnVersion: