Yes. These green/yellow lines are also for all courtesy lights that are powered up by door jamb switches or trunk lids, so you are correct...they are tied together. A similar set of wires, blue/black, can be controlled by the headlamp switch.
The single female red bullet connector is for the optional trunk light, and all 1969 underdash harnesses have this female plug. The optional harness for that would have a matching red male bullet plug.