Quick reply...
Indeed, if you wish to control the flashlight from a batch script, it would be inconvenient to have gui of Lanterne starting up - even if it shuts down after executing the commands. And it would be fairly difficult to have both visible-gui and invisible-command-line packed in one app.
So, yes. Lanterne for manual signals, and Torchio for batch mode? Something like that. For example, if you want to read the incoming SMS messages by having the bright flashlight illuminate your surroundings with Morse code, torchio is brilliant.
After all, it's fairly difficult to manually control the coloured-led: if I remember correctly, MCE gives different led sequences for different types of events, never mind what the content of the event is.
I can imagine it. An SMS comes in. The mode is 'Silent-NoScreen'. The coloured led repeats, as usually, the blue-or-whatever led blinking until you notice it at last (a short break in a meeting?). Then, you open the camera-lens-cover, and red flashlight blinks in Morse code to tell you the content of SMS. The SMS is marked 'Read' as soon as you close the cover. If you weren't able to read the Morse code from first attempt, half-press the camera button to repeat the message. If you want to reply to SMS, full-press the camera button, and it will bring up the SMS-write interface to the sender of the received SMS.
It's just a possible exaple of what can be done. I am not even sure how to do it. It would be a handy extension of hildon-notifications, though. Along with espeak reading the notification text if the mode is 'General-NoScreen'.
Best wishes.
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Per aspera ad astra...