I used Carly with no battery charger and with the engine off but the ignition on. It gives you a module count so I may try it with the engine on and see if it finds anything else.
I'd guess it's safer to do it with the battery on a charger, but for what I needed to code the programming only took a minute or so.
figured out my mirror issue I think - without the powerfold mirrors or memory seats I don't believe the car comes with the necessary harness (LIM Bus in the doors) to tilt the mirror in reverse
You can retrofit it but seems like a lot of work.