I’ve encountered a similar issue previously, and found that
I suggest you try setting channels 1 to 6 to stopped (1500) before you arm, and see if that fixes the issue 
By the way, I wasn’t aware of dronekit-python. It’s apparently a wrapper around pymavlink that tries to improve the interface, and includes documentation. It seems like an interesting project, but the development/maintenance has mostly died out since 2016 (when 3D Robotics split from the ArduPilot project, and stopped producing open-source drones).