The launcher window does not properly bind to the .desktop file that exists for it. This could most likely be fixed by setting the WM_CLASS property of the window and adding that to the .desktop file. This both causes it to not stack with the shortcut if you pin it and stops it from having an icon/name. These can both be seen in the screenshot. The icon I am hovering over with my mouse is actually the launcher, but due to the reason listed before, it does not stack with the shortcut above it.