This is just the way that the dropbox api works I think. It allows Joplin to create a single folder for that application.
Multiple target sync is really easy with something like nextcloud, all you have to do is to make a new folder called joplin2 or something.
I made some comments on this back when 2.8 hit - Joplin 2.8 is available! - #10 by Daeraxa