Taking Microsoft Office as example... When Excel is pinned to the taskbar or is pinned in a menu tab, and you right click, you see recent items and pinned items (i.e., frequently-used, or favorite, spreadsheets). However, When Excel is pinned within a FOLDER inside of a StarMenu tab, those recent and pinned items do not appear. It would be nice to see them there, too!
I'm sure other apps may have context menus that would be lost if contained within a FOLDER on the Start Menu.