Is there a way to run AutoKey in a daemon mode that is in background and without a tray icon or from a shell script ?
Run ‘autokey’ with an & while making sure that the preference (Settings->Advanced Settings) “Show a tray icon” in unselected. Now when you want to see the Configuration window again while Autokey is running in in daemon mode, you can press the Special Hotkey which you assigned in the Settings->Advanced Settings->Special Hotkeys->Use a hotkey to show configuration window.