I don’t know if this is identical behaviour to the current stable version since I never really considered using it, but in the beta version the Desktop shortcuts created by the app (coghweel next to play button -> create desktop shortcut) don’t actually start the game, they just launch the launcher and open the game’s tab.
The shortcuts should start the launcher (if not running), log-in automatically (if configured to do so) and then start the game using the same login details. Much like what happens with shortcuts to games made by eg. Steam.
There should be option to automatically minimize the launcher after launching the game, too.