Andy. You say the lighting on the side of the saddlebags are not factory installed? I'm a little confused here. All 'Wings I've come across, including the one I previously owned, have these lights??
The lights on the side of the panniers are not factory installed. They could be Hondaline or an aftermarket manufacturer. Either way they have been added and it sounds like they are wired to an Accessory (ACC) hot circuit.
Key switch has an ACC selection between OFF and RUN. This should allow you to operate the radio, air compressor, expresso machine and such without providing power to the ignition system or headlights.