The command line tool is not contained in the AppStore version because sandboxing prohibits the rights extension needed in order to install the tool.
However, you can take it simply from the version downloadable on the web site and copy it to the application bundle from the AppStore (see this image).
The only missing piece is then to make the tool available by setting an alias or link.
Does this help?
Btw: This is the only difference between AppStore and web site version. (due to sandboxing)