It actually works, my error was using the full path to the app in the 'initial-program' field of Guacamole.
So two steps :
1. Create the RDP exactly like stated in RemoteApp Tool's help.
2. Use the *name* of the created RemoteApp in the initial-program field of Guacamole, e.g. : ||notepad
(You can edit the RDP file created by RemoteApp Tool to see the name, if unsure).
That's litterally all. If your Guacamole install works otherwise, this works.
Enjoy.