That’s a good catch, and it appears that your initial instinct was potentially correct. I apologize that I don’t have enough expertise to guide the configuration further.
Here’s a somewhat recent post confirming as much in a longstanding topic by the dev who wrote much of the tiltrotor code:
What I can say for certain is that manual mode often results in red herring results. Users from pure RC flying backgrounds configure manual mode as they would without an autopilot and quickly get themselves into trouble because inputs and outputs are reversed in the wrong fashion (i.e., manual modes work, but the autopilot has no idea which way is “up” with respect to control surfaces or motor direction).