This is because GTK based systems use gvfs (Gnome Virtual file System).
If you want to mount a device in a permanent way - you should avoid /mnt as this is designated temporary mount.
What appears in the leftmost pane of Thunar is what thunar recognizes as part of gvfs or when you use the x-gvfs-show mount option.
You can of course use whatever teminology suiting you best - but if you want to eliminate trouble you should use another structure distinct from the system.