I've had my aiming controls set to manual since the first SP mission. I was also initially playing MP with manual settings.
I received an invite from a friend, joined their lobby - and was prompted that joining would change my aiming settings. It's been switched to assisted-aim ever since.
The setting is disabled and locked to assisted-aim in the pause menu and I don't see any option to change it when hosting a lobby. Has anyone figured out how to revert to manual?