Can tuning be done in an automated mission?

I am in the process of making a QuadPlane Tilt Rotor which has the ultimate goal of being flown only autonomously from mission planner. The hope is to minimize the number of manual radio-controlled flights, to none even if possible. However, to make the aircraft fly properly it must be tuned. Is it possible to do tuning during automated flights, or does autotune have to be performed during a manually controlled flight?

From the Wiki Note:
you can AutoTune in most stabilized flight modes, such as CRUISE or FBWA/B, LOITER, or even during an AUTO mission segment (if STICK_MIXING is enabled), via an RCx_OPTION switch set to 107.

ArduPlane AutoTune

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I appreciate the kinking. I am interested in hearing some personal experience or expounding on how this would actually work, if you or anyone else can provide that.

It works pretty much as the wiki says. What are you looking for?

Enable STICK_MIXING
Configure an RCx_OPTION,107
Configure a switch on your Transmitter for “x” channel.
While flying the mission flip the switch when you want to start the Auto Tune and give it stick input as you normally would for Auto Tune. When you flip the switch back it will return to the Mission.